diff --git a/NAMESPACE b/NAMESPACE
index 68f2f41..fabec76 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -131,6 +131,7 @@ export(
     ## SummarizedExperiment-class.R:
     SummarizedExperiment,
     exptData, "exptData<-",
+    rowRanges, "rowRanges<-",
     rowData, "rowData<-",
     colData, "colData<-",
     assays, "assays<-",
@@ -145,7 +146,7 @@ exportMethods(
     granges, grglist, rglist,
     SummarizedExperiment,
     exptData, "exptData<-",
-    rowData, "rowData<-",
+    rowRanges, "rowRanges<-",
     colData, "colData<-",
     assays, "assays<-",
     assay, "assay<-",
diff --git a/NEWS b/NEWS
index a4b8a8f..2fc94ed 100644
--- a/NEWS
+++ b/NEWS
@@ -4,6 +4,8 @@ CHANGES IN VERSION 1.20.0
 NEW FEATURES
 
     o Add 'assayNames', 'assayNames<-' for SummarizedExperiment
+    o Deprecate 'rowData', 'rowData<-' for SummarizedExperiment
+    o Add 'rowRanges', 'rowRanges<-' for SummarizedExperiment
 
 CHANGES IN VERSION 1.18.0
 -------------------------
diff --git a/R/SummarizedExperiment-class.R b/R/SummarizedExperiment-class.R
index d39756f..861c8c0 100644
--- a/R/SummarizedExperiment-class.R
+++ b/R/SummarizedExperiment-class.R
@@ -61,11 +61,11 @@ setClass("SummarizedExperiment",
     NULL
 }
 
-.valid.SummarizedExperiment.rowData_dims <- function(x)
+.valid.SummarizedExperiment.rowRanges_dims <- function(x)
 {
     if (!all(sapply(assays(x, withDimnames=FALSE), nrow) ==
-             length(rowData(x))))
-        return("'rowData' length differs from 'assays' nrow")
+             length(rowRanges(x))))
+        return("'rowRanges' length differs from 'assays' nrow")
     NULL
 }
 
@@ -79,7 +79,7 @@ setClass("SummarizedExperiment",
 
 .valid.SummarizedExperiment.assays_dims <- function(x)
 {
-    c(.valid.SummarizedExperiment.rowData_dims(x),
+    c(.valid.SummarizedExperiment.rowRanges_dims(x),
       .valid.SummarizedExperiment.colData_dims(x))
 }
 
@@ -204,10 +204,22 @@ setGeneric("exptData<-",
 ## rowData, colData seem too vague, but from eSet derived classes wanted to
 ## call the rows / cols something different from 'features' or 'samples', so
 ## might as well avoid the issue
-setGeneric("rowData", function(x, ...) standardGeneric("rowData"))
+setGeneric("rowRanges", function(x, ...) standardGeneric("rowRanges"))
 
-setGeneric("rowData<-",
-    function(x, ..., value) standardGeneric("rowData<-"))
+setGeneric("rowRanges<-",
+    function(x, ..., value) standardGeneric("rowRanges<-"))
+
+rowData <- function(...)
+{
+    .Deprecated("rowRanges")
+    rowRanges(...)
+}
+
+`rowData<-` <- function(x, ..., value)
+{
+    .Deprecated("rowRanges<-")
+    rowRanges(x, ...) <- value
+}
 
 setGeneric("colData", function(x, ...) standardGeneric("colData"))
 
@@ -249,24 +261,24 @@ setReplaceMethod("exptData", c("SummarizedExperiment", "list"),
     clone(x, ..., exptData=SimpleList(value))
 })
 
-setMethod(rowData, "SummarizedExperiment",
+setMethod(rowRanges, "SummarizedExperiment",
     function(x, ...) value(x, "rowData"))
 
-.SummarizedExperiment.rowData.replace <-
+.SummarizedExperiment.rowRanges.replace <-
     function(x, ..., value)
 {
     x <- clone(x, ..., rowData=value)
-    msg <- .valid.SummarizedExperiment.rowData_dims(x)
+    msg <- .valid.SummarizedExperiment.rowRanges_dims(x)
     if (!is.null(msg))
         stop(msg)
     x
 }
 
-setReplaceMethod("rowData", c("SummarizedExperiment", "GenomicRanges"),
-    .SummarizedExperiment.rowData.replace)
+setReplaceMethod("rowRanges", c("SummarizedExperiment", "GenomicRanges"),
+    .SummarizedExperiment.rowRanges.replace)
 
-setReplaceMethod("rowData", c("SummarizedExperiment", "GRangesList"),
-    .SummarizedExperiment.rowData.replace)
+setReplaceMethod("rowRanges", c("SummarizedExperiment", "GRangesList"),
+    .SummarizedExperiment.rowRanges.replace)
 
 setMethod(colData, "SummarizedExperiment",
     function(x, ...) value(x, "colData"))
@@ -392,23 +404,23 @@ setReplaceMethod("assay",
 setMethod(dim, "SummarizedExperiment",
     function(x)
 {
-    c(length(rowData(x)), nrow(colData(x)))
+    c(length(rowRanges(x)), nrow(colData(x)))
 })
 
 setMethod(dimnames, "SummarizedExperiment",
     function(x)
 {
-    list(names(rowData(x)), rownames(colData(x)))
+    list(names(rowRanges(x)), rownames(colData(x)))
 })
 
 setReplaceMethod("dimnames", c("SummarizedExperiment", "list"),
     function(x, value)
 {
-    rowData <- rowData(x)
-    names(rowData) <- value[[1]]
+    rowRanges <- rowRanges(x)
+    names(rowRanges) <- value[[1]]
     colData <- colData(x)
     rownames(colData) <- value[[2]]
-    clone(x, rowData=rowData, colData=colData)
+    clone(x, rowData=rowRanges, colData=colData)
 })
 
 setReplaceMethod("dimnames", c("SummarizedExperiment", "NULL"),
@@ -482,7 +494,7 @@ setMethod("[", c("SummarizedExperiment", "ANY", "ANY"),
     if (!missing(i) && !missing(j)) {
         ii <- as.vector(i)
         jj <- as.vector(j)
-        x <- clone(x, ..., rowData=rowData(x)[i],
+        x <- clone(x, ..., rowData=rowRanges(x)[i],
             colData=colData(x)[j, , drop=FALSE],
             assays=.SummarizedExperiment.assays.subset(x, ii, jj))
     } else if (missing(i)) {
@@ -491,7 +503,7 @@ setMethod("[", c("SummarizedExperiment", "ANY", "ANY"),
             assays=.SummarizedExperiment.assays.subset(x, j=jj))
     } else {                            # missing(j)
         ii <- as.vector(i)
-        x <- clone(x, ..., rowData=rowData(x)[i],
+        x <- clone(x, ..., rowData=rowRanges(x)[i],
             assays=.SummarizedExperiment.assays.subset(x, ii))
     }
     x
@@ -553,9 +565,9 @@ setReplaceMethod("[",
         jj <- as.vector(j)
         x <- clone(x, ..., exptData=c(exptData(x), exptData(value)),
             rowData=local({
-                r <- rowData(x)
-                r[i] <- rowData(value)
-                names(r)[ii] <- names(rowData(value))
+                r <- rowRanges(x)
+                r[i] <- rowRanges(value)
+                names(r)[ii] <- names(rowRanges(value))
                 r
             }), colData=local({
                 c <- colData(x)
@@ -580,13 +592,13 @@ setReplaceMethod("[",
         ii <- as.vector(i)
         x <- clone(x, ..., exptData=c(exptData(x), exptData(value)),
             rowData=local({
-                r <- rowData(x)
-                r[i] <- rowData(value)
-                names(r)[ii] <- names(rowData(value))
+                r <- rowRanges(x)
+                r[i] <- rowRanges(value)
+                names(r)[ii] <- names(rowRanges(value))
                 r
             }), assays=.SummarizedExperiment.assays.subsetgets(x, ii,
                   ..., value=value))
-        msg <- .valid.SummarizedExperiment.rowData_dims(x)
+        msg <- .valid.SummarizedExperiment.rowRanges_dims(x)
     }
     if (!is.null(msg))
         stop(msg)
@@ -609,13 +621,12 @@ setMethod("rbind", "SummarizedExperiment",
             stop("'...' objects must have the same colnames")
     if (!.compare(lapply(args, ncol)))
             stop("'...' objects must have the same number of samples")
-    rowData <- do.call(c, lapply(args,
-        function(i) slot(i, "rowData")))
+    rowRanges <- do.call(c, lapply(args, rowRanges))
     colData <- .cbind.DataFrame(args, colData, "colData")
     assays <- .bind.arrays(args, rbind, "assays")
     exptData <- do.call(c, lapply(args, exptData))
 
-    initialize(args[[1]], assays=assays, rowData=rowData,
+    initialize(args[[1]], assays=assays, rowData=rowRanges,
                colData=colData, exptData=exptData)
 }
 
@@ -629,15 +640,15 @@ setMethod("cbind", "SummarizedExperiment",
 
 .cbind.SummarizedExperiment <- function(args)
 {
-    if (!.compare(lapply(args, rowData), TRUE))
+    if (!.compare(lapply(args, rowRanges), TRUE))
         stop("'...' object ranges (rows) are not compatible")
-    rowData <- rowData(args[[1]])
-    mcols(rowData) <- .cbind.DataFrame(args, mcols, "mcols")
+    rowRanges <- rowRanges(args[[1]])
+    mcols(rowRanges) <- .cbind.DataFrame(args, mcols, "mcols")
     colData <- do.call(rbind, lapply(args, colData))
     assays <- .bind.arrays(args, cbind, "assays")
     exptData <- do.call(c, lapply(args, exptData))
 
-    initialize(args[[1]], assays=assays, rowData=rowData,
+    initialize(args[[1]], assays=assays, rowData=rowRanges,
                colData=colData, exptData=exptData)
 }
 
@@ -793,8 +804,8 @@ setMethod(show, "SummarizedExperiment",
     dlen <- sapply(dimnames, length)
     if (dlen[[1]]) scat("rownames(%d): %s\n", dimnames[[1]])
     else scat("rownames: NULL\n")
-    scat("rowData metadata column names(%d): %s\n",
-         names(mcols(rowData(object))))
+    scat("rowRanges metadata column names(%d): %s\n",
+         names(mcols(rowRanges(object))))
     if (dlen[[2]]) scat("colnames(%d): %s\n", dimnames[[2]])
     else cat("colnames: NULL\n")
     scat("colData names(%d): %s\n", names(colData(object)))
diff --git a/R/SummarizedExperiment-rowData-methods.R b/R/SummarizedExperiment-rowData-methods.R
index fb583bf..7f24042 100644
--- a/R/SummarizedExperiment-rowData-methods.R
+++ b/R/SummarizedExperiment-rowData-methods.R
@@ -14,14 +14,14 @@
 setMethod(mcols, "SummarizedExperiment",
     function(x, use.names=FALSE, ...)
 {
-    mcols(rowData(x), use.names=use.names, ...)
+    mcols(rowRanges(x), use.names=use.names, ...)
 })
 
 setReplaceMethod("mcols", "SummarizedExperiment",
     function(x, ..., value)
 {
     clone(x, rowData=local({
-        r <- rowData(x)
+        r <- rowRanges(x)
         mcols(r) <- value
         r
     }))
@@ -33,26 +33,26 @@ setReplaceMethod("mcols", "SummarizedExperiment",
 setMethod(elementMetadata, "SummarizedExperiment",
     function(x, use.names=FALSE, ...)
 {
-    elementMetadata(rowData(x), use.names=use.names, ...)
+    elementMetadata(rowRanges(x), use.names=use.names, ...)
 })
 
 setReplaceMethod("elementMetadata", "SummarizedExperiment",
     function(x, ..., value)
 {
-    elementMetadata(rowData(x), ...) <- value
+    elementMetadata(rowRanges(x), ...) <- value
     x
 })
 
 setMethod(values, "SummarizedExperiment",
     function(x, ...)
 {
-    values(rowData(x), ...)
+    values(rowRanges(x), ...)
 })
 
 setReplaceMethod("values", "SummarizedExperiment",
     function(x, ..., value)
 {
-    values(rowData(x), ...) <- value
+    values(rowRanges(x), ...) <- value
     x
 })
 
@@ -75,10 +75,10 @@ local({
         formals(tmpl) <- formals(generic)
         fmls <- as.list(formals(tmpl))
         fmls[] <- sapply(names(fmls), as.symbol)
-        fmls[[generic@signature]] <- quote(rowData(x))
+        fmls[[generic@signature]] <- quote(rowRanges(x))
         if (.fun %in% endomorphisms)
             body(tmpl) <- substitute({
-                rowData(x) <- do.call(FUN, ARGS)
+                rowRanges(x) <- do.call(FUN, ARGS)
                 x
             }, list(FUN=.fun, ARGS=fmls))
         else
@@ -95,7 +95,7 @@ setMethod("granges", "SummarizedExperiment",
     if (!identical(use.mcols, FALSE))
         stop("\"granges\" method for SummarizedExperiment objects ",
              "does not support the 'use.mcols' argument")
-    rowData(x)
+    rowRanges(x)
 })
 
 ## 2-argument dispatch:
@@ -108,9 +108,9 @@ setMethod("granges", "SummarizedExperiment",
     function(x, y)
 {
     if (is(x, "SummarizedExperiment"))
-        x <- rowData(x)
+        x <- rowRanges(x)
     if (is(y, "SummarizedExperiment"))
-        y <- rowData(y)
+        y <- rowRanges(y)
     compare(x, y)
 }
 
@@ -118,9 +118,9 @@ setMethod("granges", "SummarizedExperiment",
     function(e1, e2)
 {
     if (is(e1, "SummarizedExperiment"))
-        e1 <- rowData(e1)
+        e1 <- rowRanges(e1)
     if (is(e2, "SummarizedExperiment"))
-        e2 <- rowData(e2)
+        e2 <- rowRanges(e2)
     callGeneric(e1=e1, e2=e2)
 }
 
@@ -129,7 +129,7 @@ setMethod("granges", "SummarizedExperiment",
              algorithm = c("nclist", "intervaltree"), ignore.strand = FALSE)
 {
     select <- match.arg(select)
-    x <- rowData(x)
+    x <- rowRanges(x)
     nearest(x=x, select=select,
             algorithm=match.arg(algorithm), ignore.strand=ignore.strand)
 }
@@ -138,9 +138,9 @@ setMethod("granges", "SummarizedExperiment",
     function(x, y, ignore.strand = FALSE, ...)
 {
     if (is(x, "SummarizedExperiment"))
-        x <- rowData(x)
+        x <- rowRanges(x)
     if (is(y, "SummarizedExperiment"))
-        y <- rowData(y)
+        y <- rowRanges(y)
     distance(x, y, ignore.strand=ignore.strand, ...)
 }
 
@@ -149,9 +149,9 @@ setMethod("granges", "SummarizedExperiment",
              ignore.strand = FALSE, ...)
 {
     if (is(x, "SummarizedExperiment"))
-        x <- rowData(x)
+        x <- rowRanges(x)
     if (is(subject, "SummarizedExperiment"))
-        subject <- rowData(subject)
+        subject <- rowRanges(subject)
     distanceToNearest(x, subject, algorithm=match.arg(algorithm),
                       ignore.strand=ignore.strand, ...)
 }
@@ -171,9 +171,9 @@ local({
             body(tmpl) <- substitute({
                 select <- match.arg(select)
                 if (is(x, "SummarizedExperiment"))
-                    x <- rowData(x)
+                    x <- rowRanges(x)
                 if (is(subject, "SummarizedExperiment"))
-                    subject <- rowData(subject)
+                    subject <- rowRanges(subject)
                 FUN(x=x, subject=subject, select=select,
                     ignore.strand=ignore.strand)
             }, list(FUN=as.symbol(.fun)))
@@ -188,9 +188,9 @@ local({
             body(tmpl) <- substitute({
                 select <- match.arg(select)
                 if (is(x, "SummarizedExperiment"))
-                    x <- rowData(x)
+                    x <- rowRanges(x)
                 if (is(subject, "SummarizedExperiment"))
-                    subject <- rowData(subject)
+                    subject <- rowRanges(subject)
                 FUN(x=x, subject=subject, select=select,
                     ignore.strand=ignore.strand)
             }, list(FUN=as.symbol(.fun)))
@@ -211,14 +211,14 @@ local({
 setReplaceMethod("strand", "SummarizedExperiment",
     function(x, ..., value)
 {
-    strand(rowData(x)) <- value
+    strand(rowRanges(x)) <- value
     x
 })
 
 setReplaceMethod("ranges", "SummarizedExperiment",
     function(x, ..., value)
 {
-    ranges(rowData(x)) <- value
+    ranges(rowRanges(x)) <- value
     x
 })
 
@@ -227,7 +227,7 @@ setReplaceMethod("ranges", "SummarizedExperiment",
 setMethod("order", "SummarizedExperiment",
     function(..., na.last = TRUE, decreasing = FALSE)
 {
-    args <- lapply(list(...), rowData)
+    args <- lapply(list(...), rowRanges)
     do.call("order",
             c(args, list(na.last=na.last, decreasing=decreasing)))
 })
@@ -237,13 +237,13 @@ setMethod("rank", "SummarizedExperiment",
               ties.method = c("average", "first", "random", "max", "min"))
 {
     ties.method <- match.arg(ties.method)
-    rank(rowData(x), na.last=na.last, ties.method=ties.method)
+    rank(rowRanges(x), na.last=na.last, ties.method=ties.method)
 })
 
 setMethod("sort", "SummarizedExperiment",
     function(x, decreasing = FALSE, ...)
 {
-    x[order(rowData(x), decreasing=decreasing),]
+    x[order(rowRanges(x), decreasing=decreasing),]
 })
 
 ## subset
@@ -251,7 +251,7 @@ setMethod("sort", "SummarizedExperiment",
 setMethod("subset", "SummarizedExperiment",
     function(x, subset, select, ...)
 {
-    i <- S4Vectors:::evalqForSubset(subset, rowData(x), ...)
+    i <- S4Vectors:::evalqForSubset(subset, rowRanges(x), ...)
     j <- S4Vectors:::evalqForSubset(select, colData(x), ...)
     x[i, j]
 })
diff --git a/R/findOverlaps-methods.R b/R/findOverlaps-methods.R
index 013ccfa..e59e257 100644
--- a/R/findOverlaps-methods.R
+++ b/R/findOverlaps-methods.R
@@ -535,7 +535,7 @@ setMethod("findOverlaps", c("SummarizedExperiment", "Vector"),
              algorithm=c("nclist", "intervaltree"),
              ignore.strand=FALSE)
     {
-        findOverlaps(rowData(query), subject,
+        findOverlaps(rowRanges(query), subject,
                      maxgap=maxgap, minoverlap=minoverlap,
                      type=match.arg(type), select=match.arg(select),
                      algorithm=match.arg(algorithm),
@@ -550,7 +550,7 @@ setMethod("findOverlaps", c("Vector", "SummarizedExperiment"),
              algorithm=c("nclist", "intervaltree"),
              ignore.strand=FALSE)
     {
-        findOverlaps(query, rowData(subject),
+        findOverlaps(query, rowRanges(subject),
                      maxgap=maxgap, minoverlap=minoverlap,
                      type=match.arg(type), select=match.arg(select),
                      algorithm=match.arg(algorithm),
@@ -565,7 +565,7 @@ setMethod("findOverlaps", c("SummarizedExperiment", "SummarizedExperiment"),
              algorithm=c("nclist", "intervaltree"),
              ignore.strand=FALSE)
     {
-        findOverlaps(rowData(query), rowData(subject),
+        findOverlaps(rowRanges(query), rowRanges(subject),
                      maxgap=maxgap, minoverlap=minoverlap,
                      type=match.arg(type), select=match.arg(select),
                      algorithm=match.arg(algorithm),
diff --git a/TODO.md b/TODO.md
index 6f95f78..44c314b 100644
--- a/TODO.md
+++ b/TODO.md
@@ -2,7 +2,7 @@
 
 Long term
 - Separate package
-- Separate classes for 'DataFrame' and '*Ranges' rowData
+- Separate classes for 'DataFrame' and '\*Ranges' rowData
 
 Immediate
 
@@ -11,7 +11,7 @@ Immediate
 
 Short term (start of next release cycle)
 
-3. Implement separate classes for DataFrame and *Ranges rowData()
+3. Implement separate classes for DataFrame and \*Ranges rowData()
 
 Possibilities?
 
@@ -22,14 +22,14 @@ Possibilities?
 
   - SummarizedExperimentGR
     @rowRanges: *Ranges; rowData() == mcols(rowRanges())
- 
+
 - SummarizedExperiment as 'DataFrame' base class,
   SummarizedExperimentGR as derived class
-  
+
   - SummarizedExperiment
     @rowData: DataFrame
 
   - SummarizedExperimentGR
-    @rowRanges: *Ranges; no mcols() (rowData() from inheritted
+    @rowRanges: \*Ranges; no mcols() (rowData() from inheritted
     @rowData)
 
diff --git a/inst/unitTests/test_SummarizedExperiment-class.R b/inst/unitTests/test_SummarizedExperiment-class.R
index 2c11ed8..e4533e1 100644
--- a/inst/unitTests/test_SummarizedExperiment-class.R
+++ b/inst/unitTests/test_SummarizedExperiment-class.R
@@ -2,21 +2,21 @@ m <- matrix(1, 5, 3, dimnames=list(NULL, NULL))
 mlst <- matrix(1, 3, 3, dimnames=list(NULL, NULL))
 mList <- list(m, mlst)
 assaysList <- list(gr=SimpleList(m=m), grl=SimpleList(m=mlst))
-rowDataList <- 
+rowRangesList <- 
     list(gr=GRanges("chr1", IRanges(1:5, 10)), 
          grl=split(GRanges("chr1", IRanges(1:5, 10)), c(1,1,2,2,3)))
-names(rowDataList[["grl"]]) <- NULL
+names(rowRangesList[["grl"]]) <- NULL
 colData <- DataFrame(x=letters[1:3])
 
 ## a list of one SE with GRanges and one with GRangesList
 ssetList <- 
     list(SummarizedExperiment(
            assays=assaysList[["gr"]], 
-           rowData=rowDataList[["gr"]], 
+           rowData=rowRangesList[["gr"]], 
            colData=colData),
          SummarizedExperiment(
            assays=assaysList[["grl"]], 
-           rowData=rowDataList[["grl"]], 
+           rowData=rowRangesList[["grl"]], 
            colData=colData))
 
 
@@ -42,7 +42,7 @@ test_SummarizedExperiment_construction <- function() {
         sset <- ssetList[[i]] 
         checkTrue(validObject(sset))
         checkIdentical(SimpleList(m=mList[[i]]), assays(sset))
-        checkIdentical(rowDataList[[i]], rowData(sset))
+        checkIdentical(rowRangesList[[i]], rowRanges(sset))
         checkIdentical(DataFrame(x=letters[1:3]), colData(sset))
     }
 
@@ -66,13 +66,13 @@ test_SummarizedExperiment_construction <- function() {
 test_SummarizedExperiment_getters <- function() {
     for (i in length(ssetList)) {
         sset <- ssetList[[i]] 
-        rowData <- rowDataList[[i]] 
+        rowRanges <- rowRangesList[[i]] 
         ## dim, dimnames
-        checkIdentical(c(length(rowData), nrow(colData)), dim(sset))
+        checkIdentical(c(length(rowRanges), nrow(colData)), dim(sset))
         checkIdentical(list(NULL, NULL), dimnames(sset))
 
         ## row / col / exptData
-        checkIdentical(rowData, rowData(sset))
+        checkIdentical(rowRanges, rowRanges(sset))
         checkIdentical(colData, colData(sset))
         checkIdentical(SimpleList(), exptData(sset))
     }
@@ -105,13 +105,13 @@ test_SummarizedExperiment_setters <- function()
 {
     for (i in length(ssetList)) {
         sset <- ssetList[[i]] 
-        rowData <- rowDataList[[i]] 
+        rowRanges <- rowRangesList[[i]] 
         ## row / col / exptData<-
         ss1 <- sset
-        revData <- rowData[rev(seq_len(length(rowData))),,drop=FALSE]
-        rowData(ss1) <- revData
-        checkIdentical(revData, rowData(ss1))
-        checkException(rowData(ss1) <- rowData(sset)[1:2,,drop=FALSE],
+        revData <- rowRanges[rev(seq_len(length(rowRanges))),,drop=FALSE]
+        rowRanges(ss1) <- revData
+        checkIdentical(revData, rowRanges(ss1))
+        checkException(rowRanges(ss1) <- rowRanges(sset)[1:2,,drop=FALSE],
                        "incorrect row dimensions", TRUE)
         revData <- colData[rev(seq_len(nrow(colData))),,drop=FALSE]
         colData(ss1) <- revData
@@ -140,9 +140,9 @@ test_SummarizedExperiment_setters <- function()
         rownames(ss1) <- dimnames[[1]]
         colnames(ss1) <- dimnames[[2]]
         checkIdentical(dimnames, dimnames(ss1))
-        rowData1 <- rowData
-        names(rowData1) <- dimnames[[1]]
-        checkIdentical(rowData1, rowData(ss1))
+        rowRanges1 <- rowRanges
+        names(rowRanges1) <- dimnames[[1]]
+        checkIdentical(rowRanges1, rowRanges(ss1))
         colData1 <- colData
         row.names(colData1) <- dimnames[[2]]
         checkIdentical(colData1, colData(ss1))
@@ -158,19 +158,19 @@ test_SummarizedExperiment_subset <- function()
 {
     for (i in length(ssetList)) {
         sset <- ssetList[[i]] 
-        rowData <- rowDataList[[i]] 
+        rowRanges <- rowRangesList[[i]] 
         ## numeric
         ss1 <- sset[2:3,]
         checkIdentical(c(2L, ncol(sset)), dim(ss1))
-        checkIdentical(rowData(ss1), rowData(sset)[2:3,])
+        checkIdentical(rowRanges(ss1), rowRanges(sset)[2:3,])
         checkIdentical(colData(ss1), colData(sset))
         ss1 <- sset[,2:3]
         checkIdentical(c(nrow(sset), 2L), dim(ss1))
-        checkIdentical(rowData(ss1), rowData(sset))
+        checkIdentical(rowRanges(ss1), rowRanges(sset))
         checkIdentical(colData(ss1), colData(sset)[2:3,,drop=FALSE])
         ss1 <- sset[2:3, 2:3]
         checkIdentical(c(2L, 2L), dim(ss1))
-        checkIdentical(rowData(ss1), rowData(sset)[2:3,,drop=FALSE])
+        checkIdentical(rowRanges(ss1), rowRanges(sset)[2:3,,drop=FALSE])
         checkIdentical(colData(ss1), colData(sset)[2:3,,drop=FALSE])
 
         ## character
@@ -178,8 +178,8 @@ test_SummarizedExperiment_subset <- function()
         dimnames(ss1) <- list(LETTERS[seq_len(nrow(ss1))],
                                letters[seq_len(ncol(ss1))])
         ridx <- c("B", "C")
-        checkIdentical(rowData(ss1[ridx,]), rowData(ss1)[ridx,])
-        checkIdentical(rowData(ss1["C",]), rowData(ss1)["C",,drop=FALSE])
+        checkIdentical(rowRanges(ss1[ridx,]), rowRanges(ss1)[ridx,])
+        checkIdentical(rowRanges(ss1["C",]), rowRanges(ss1)["C",,drop=FALSE])
         checkException(ss1[LETTERS,], "i-index out of bounds", TRUE)
         cidx <- c("b", "c")
         checkIdentical(colData(ss1[,cidx]), colData(ss1)[cidx,,drop=FALSE])
@@ -196,14 +196,14 @@ test_SummarizedExperiment_subset <- function()
         checkIdentical(c(nrow(ss1), 0L), dim(ss1[,FALSE]))
         idx <- c(TRUE, FALSE)               # recycling
         ss2 <- ss1[idx,]
-        checkIdentical(rowData(ss1)[idx,,drop=FALSE], rowData(ss2))
+        checkIdentical(rowRanges(ss1)[idx,,drop=FALSE], rowRanges(ss2))
         ss2 <- ss1[,idx]
         checkIdentical(colData(ss1)[idx,,drop=FALSE], colData(ss2))
 
         ## Rle
         ss1 <- sset
         rle <- rep(c(TRUE, FALSE), each=3, length.out=nrow(ss1))
-        checkIdentical(rowData(ss1[rle]), rowData(ss1[Rle(rle)]))
+        checkIdentical(rowRanges(ss1[rle]), rowRanges(ss1[Rle(rle)]))
         checkIdentical(assays(ss1[rle]), assays(ss1[Rle(rle)]))
     }
 
@@ -224,8 +224,8 @@ test_SummarizedExperiment_subsetassign <- function()
         ## rows
         ss1 <- sset
         ss1[1:2,] <- ss1[2:1,]
-        checkIdentical(rowData(sset)[2:1,], rowData(ss1)[1:2,])
-        checkIdentical(rowData(sset[-(1:2),]), rowData(ss1)[-(1:2),])
+        checkIdentical(rowRanges(sset)[2:1,], rowRanges(ss1)[1:2,])
+        checkIdentical(rowRanges(sset[-(1:2),]), rowRanges(ss1)[-(1:2),])
         checkIdentical(colData(sset), colData(ss1))
         checkIdentical(c(exptData(sset), exptData(sset)), exptData(ss1))
         ## Rle
@@ -233,7 +233,7 @@ test_SummarizedExperiment_subsetassign <- function()
         rle <- rep(c(TRUE, FALSE), each=3, length.out=nrow(ss1))
         ss1rle[rle,] <- ss1rle[rle,]
         ss1Rle[Rle(rle),] <- ss1Rle[Rle(rle),]
-        checkIdentical(rowData(ss1rle), rowData(ss1Rle))
+        checkIdentical(rowRanges(ss1rle), rowRanges(ss1Rle))
         checkIdentical(assays(ss1rle), assays(ss1Rle))
         ## cols
         ss1 <- sset
@@ -242,12 +242,12 @@ test_SummarizedExperiment_subsetassign <- function()
                        colData(ss1)[1:2,,drop=FALSE])
         checkIdentical(colData(sset)[-(1:2),,drop=FALSE],
                        colData(ss1)[-(1:2),,drop=FALSE])
-        checkIdentical(rowData(sset), rowData(ss1))
+        checkIdentical(rowRanges(sset), rowRanges(ss1))
         checkIdentical(c(exptData(sset), exptData(sset)), exptData(ss1))
     }
     ## full replacement
     ss1 <- ss2 <- ssetList[[1]]
-    rowData(ss2) <- rev(rowData(ss2))
+    rowRanges(ss2) <- rev(rowRanges(ss2))
     ss1[,] <- ss2
     checkIdentical(ss1, ss2)
 }
@@ -274,11 +274,11 @@ test_SummarizedExperiment_cbind <- function()
     res <- cbind(se1, se2)
     checkTrue(nrow(res) == 5)
     checkTrue(ncol(res) == 5)
-    ## rowData
+    ## rowRanges
     mcols(se1) <- DataFrame("one"=1:5)
     mcols(se2) <- DataFrame("two"=6:10)
     res <- quiet(cbind(se1, se2))
-    checkIdentical(names(mcols(rowData(res))), c("one", "two"))
+    checkIdentical(names(mcols(rowRanges(res))), c("one", "two"))
     mcols(se2) <- DataFrame("one"=6:10, "two"=6:10)
     checkException(cbind(se1, se2), silent=TRUE)
     ## colData
@@ -319,7 +319,7 @@ test_SummarizedExperiment_rbind <- function()
     res <- rbind(se1, se2)
     checkTrue(nrow(res) == 10)
     checkTrue(ncol(res) == 3)
-    ## rowData
+    ## rowRanges
     mcols(se1) <- DataFrame("one"=1:5)
     mcols(se2) <- DataFrame("two"=6:10)
     checkException(rbind(se1, se2), silent=TRUE)
diff --git a/inst/unitTests/test_SummarizedExperiment-rowData-methods.R b/inst/unitTests/test_SummarizedExperiment-rowData-methods.R
index 7670d19..e1e9f5b 100644
--- a/inst/unitTests/test_SummarizedExperiment-rowData-methods.R
+++ b/inst/unitTests/test_SummarizedExperiment-rowData-methods.R
@@ -18,21 +18,21 @@ m <- matrix(1, 5, 3, dimnames=list(NULL, NULL))
 mlst <- matrix(1, 3, 3, dimnames=list(NULL, NULL))
 mList <- list(m, mlst)
 assaysList <- list(gr=SimpleList(m=m), grl=SimpleList(m=mlst))
-rowDataList <- 
+rowRangesList <- 
     list(gr=GRanges("chr1", IRanges(1:5, 10)), 
          grl=split(GRanges("chr1", IRanges(1:5, 10)), c(1,1,2,2,3)))
-names(rowDataList[["grl"]]) <- NULL
+names(rowRangesList[["grl"]]) <- NULL
 colData <- DataFrame(x=letters[1:3])
 
 ## a list of one SE with GRanges and one with GRangesList
 ssetList <- 
     list(SummarizedExperiment(
            assays=assaysList[["gr"]], 
-           rowData=rowDataList[["gr"]], 
+           rowData=rowRangesList[["gr"]], 
            colData=colData),
          SummarizedExperiment(
            assays=assaysList[["grl"]], 
-           rowData=rowDataList[["grl"]], 
+           rowData=rowRangesList[["grl"]], 
            colData=colData))
 
 test_SummarizedExperiment_GRanges_API <- function() {
@@ -92,16 +92,16 @@ test_SummarizedExperiment_GRanges_values <- function()
     }
 
     for (.fun in needArgs) {
-        ## all needArgs operate on rowData
+        ## all needArgs operate on rowRanges
         generic <- getGeneric(.fun)
-        x1 <- x; rowData(x1) <- generic(rowData(x1), 5)
+        x1 <- x; rowRanges(x1) <- generic(rowRanges(x1), 5)
         checkIdentical(x1, generic(x, 5))
     }
     ## isEndomorphism
     for (.fun in isEndomorphism) {
         generic <- getGeneric(.fun)
         obs <- generic(x)
-        checkIdentical(generic(rowData(x)), rowData(obs))
+        checkIdentical(generic(rowRanges(x)), rowRanges(obs))
         checkIdentical(assays(x), assays(obs))
     }
 
@@ -110,14 +110,14 @@ test_SummarizedExperiment_GRanges_values <- function()
     x1 <- shift(x, seq_len(nrow(x)) * 5)
     for (.fun in .funs) {
         generic <- getGeneric(.fun)
-        exp <- generic(rowData(x1), rowData(x1))
+        exp <- generic(rowRanges(x1), rowRanges(x1))
         obs <- generic(x1, x1)
         checkIdentical(obs, exp)
     }
     # nearest,SummarizedExperiment,missing-method
-    checkIdentical(nearest(rowData(x1)), nearest(x1)) 
-    checkIdentical(subsetByOverlaps(rowData(x1), rowData(x1)[3]),
-                   rowData(subsetByOverlaps(x1, x1[3])))
+    checkIdentical(nearest(rowRanges(x1)), nearest(x1)) 
+    checkIdentical(subsetByOverlaps(rowRanges(x1), rowRanges(x1)[3]),
+                   rowRanges(subsetByOverlaps(x1, x1[3])))
 }
 
 test_SummarizedExperiment_split <- function() {
diff --git a/man/SummarizedExperiment-class.Rd b/man/SummarizedExperiment-class.Rd
index 3e9f793..1831ea0 100644
--- a/man/SummarizedExperiment-class.Rd
+++ b/man/SummarizedExperiment-class.Rd
@@ -36,11 +36,11 @@
 \alias{assayNames,SummarizedExperiment-method}
 \alias{assayNames<-}
 \alias{assayNames<-,SummarizedExperiment,character-method}
-\alias{rowData}
-\alias{rowData,SummarizedExperiment-method}
-\alias{rowData<-}
-\alias{rowData<-,SummarizedExperiment,GenomicRanges-method}
-\alias{rowData<-,SummarizedExperiment,GRangesList-method}
+\alias{rowRanges}
+\alias{rowRanges,SummarizedExperiment-method}
+\alias{rowRanges<-}
+\alias{rowRanges<-,SummarizedExperiment,GenomicRanges-method}
+\alias{rowRanges<-,SummarizedExperiment,GRangesList-method}
 \alias{colData}
 \alias{colData,SummarizedExperiment-method}
 \alias{colData<-}
@@ -174,8 +174,8 @@ assays(x, ..., withDimnames=TRUE)
 assays(x, ..., withDimnames=TRUE) <- value
 assay(x, i, ...)
 assay(x, i, ...) <- value
-rowData(x, ...)
-rowData(x, ...) <- value
+rowRanges(x, ...)
+rowRanges(x, ...) <- value
 colData(x, ...)
 colData(x, ...) <- value
 exptData(x, ...)
@@ -218,7 +218,7 @@ exptData(x, ...) <- value
   \item{assays}{A \code{list} or \code{SimpleList} of matrix elements,
     or a \code{matrix}. All elements of the list must have the same
     dimensions, and dimension names (if present) must be consistent
-    across elements and with the row names of \code{rowData} and
+    across elements and with the row names of \code{rowRanges} and
     \code{colData}.}
 
   \item{rowData}{A \code{GRanges} or \code{GRangesList} instance describing 
@@ -258,7 +258,7 @@ exptData(x, ...) <- value
 
     For \code{[,SummarizedExperiment}, \code{[,SummarizedExperiment<-},
     \code{i}, \code{j} are instances that can act to subset the
-    underlying \code{rowData}, \code{colData}, and \code{matrix}
+    underlying \code{rowRanges}, \code{colData}, and \code{matrix}
     elements of \code{assays}.
 
     For \code{[[,SummarizedExperiment},
@@ -269,7 +269,7 @@ exptData(x, ...) <- value
   }
 
   \item{subset}{An expression which, when evaluated in the
-    context of \code{rowData(x)}, is a logical vector indicating
+    context of \code{rowRanges(x)}, is a logical vector indicating
     elements or rows to keep: missing values are taken as false.}
 
   \item{select}{An expression which, when evaluated in the
@@ -314,7 +314,7 @@ exptData(x, ...) <- value
   (in genomic coordinates) of interest. The ranges of interest are
   described by a \code{\linkS4class{GRanges}-class} or a
   \code{\linkS4class{GRangesList}-class} instance, accessible using the
-  \code{rowData} function, described below. The \code{GRanges} and
+  \code{rowRanges} function, described below. The \code{GRanges} and
   \code{GRangesList} classes contains sequence (e.g., chromosome) name,
   genomic coordinates, and strand information. Each range can be
   annotated with additional data; this data might be used to describe
@@ -412,7 +412,7 @@ exptData(x, ...) <- value
     \item{\code{assayNames(x)}, \code{assayNames(x) <- value}:}{Get or
      set the names of \code{assay()} elements.}
 
-    \item{\code{rowData(x)}, \code{rowData(x) <- value}:}{Get or set the
+    \item{\code{rowRanges(x)}, \code{rowRanges(x) <- value}:}{Get or set the
       row data. \code{value} is a \code{GenomicRanges} instance. Row
       names of \code{value} must be NULL or consistent with the existing
       row names of \code{x}.}
@@ -445,7 +445,7 @@ exptData(x, ...) <- value
   Many \code{\linkS4class{GRanges}-class} and
   \code{\linkS4class{GRangesList}-class} operations are supported on
   \sQuote{SummarizedExperiment} and derived instances, using
-  \code{rowData}.
+  \code{rowRanges}.
 
   Supported operations include: \code{\link{compare}},
   \code{\link{countOverlaps}}, \code{\link{coverage}},
@@ -492,7 +492,7 @@ exptData(x, ...) <- value
 
     \item{\code{subset(x, subset, select)}:}{Create a subset of \code{x}
       using an expression \code{subset} referring to columns of
-      \code{rowData(x)} (including \sQuote{seqnames}, \sQuote{start},
+      \code{rowRanges(x)} (including \sQuote{seqnames}, \sQuote{start},
       \sQuote{end}, \sQuote{width}, \sQuote{strand}, and
       \code{names(mcols(x))}) and / or \code{select} referring to
       column names of \code{colData(x)}.}
@@ -522,13 +522,13 @@ exptData(x, ...) <- value
   \describe{
 
     \item{\code{cbind(...)}, \code{rbind(...)}:}{
-      \code{cbind} combines objects with identical ranges (\code{rowData}) 
+      \code{cbind} combines objects with identical ranges (\code{rowRanges}) 
       but different samples (columns in \code{assays}). The colnames in
       \code{colData} must match or an error is thrown. Duplicate columns
-      of \code{mcols(rowData(SummarizedExperiment))} must contain the same
+      of \code{mcols(rowRanges(SummarizedExperiment))} must contain the same
       data. 
 
-      \code{rbind} combines objects with different ranges (\code{rowData}) 
+      \code{rbind} combines objects with different ranges (\code{rowRanges}) 
       and the same subjects (columns in \code{assays}). Duplicate columns
       of \code{colData} must contain the same data. 
 
@@ -604,13 +604,13 @@ exptData(x, ...) <- value
 \examples{
   nrows <- 200; ncols <- 6
   counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
-  rowData <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
+  rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
                      IRanges(floor(runif(200, 1e5, 1e6)), width=100),
                      strand=sample(c("+", "-"), 200, TRUE))
   colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
                        row.names=LETTERS[1:6])
   sset <- SummarizedExperiment(assays=SimpleList(counts=counts),
-                 rowData=rowData, colData=colData)
+                 rowData=rowRanges, colData=colData)
   sset
   assayNames(sset)
   assays(sset) <- endoapply(assays(sset), asinh)
diff --git a/vignettes/GenomicRangesHOWTOs.Rnw b/vignettes/GenomicRangesHOWTOs.Rnw
index 42bf02a..7c233be 100644
--- a/vignettes/GenomicRangesHOWTOs.Rnw
+++ b/vignettes/GenomicRangesHOWTOs.Rnw
@@ -585,7 +585,7 @@ identical(length(exbygene), length(assays(se)$counts))
 A copy of \Rcode{exbygene} is stored in the \Rcode{rowData} slot:
 
 <<count_6>>=
-rowData(se)
+rowRanges(se)
 @
 
 Two popular packages for RNA-Seq differential gene expression are