diff --git a/CHANGELOG.md b/CHANGELOG.md
index dbdc3d4c..065c0577 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,8 @@ net.arrange_in_layers([3,3])
 net.vis()
 ```
 
+- Allow parameter sharing for groups of different sizes, i.e. due to inhomogenous numbers of compartments or for synapses with the same (pre-)synaptic parameters but different numbers of post-synaptic partners. (#514, @jnsbck)
+
 # 0.5.0
 
 ### API changes
diff --git a/jaxley/modules/base.py b/jaxley/modules/base.py
index 59ccbd5c..2893f983 100644
--- a/jaxley/modules/base.py
+++ b/jaxley/modules/base.py
@@ -1058,9 +1058,6 @@ def make_trainable(
         ncomps_per_branch = (
             self.base.nodes["global_branch_index"].value_counts().to_numpy()
         )
-        assert np.all(
-            ncomps_per_branch == ncomps_per_branch[0]
-        ), "Parameter sharing is not allowed for modules containing branches with different numbers of compartments."
 
         data = self.nodes if key in self.nodes.columns else None
         data = self.edges if key in self.edges.columns else data
@@ -1075,14 +1072,31 @@ def make_trainable(
         grouped_view = data.groupby("controlled_by_param")
         # Because of this `x.index.values` we cannot support `make_trainable()` on
         # the module level for synapse parameters (but only for `SynapseView`).
-        inds_of_comps = list(
+        comp_inds = list(
             grouped_view.apply(lambda x: x.index.values, include_groups=False)
         )
-        indices_per_param = jnp.stack(inds_of_comps)
+
+        # check if all shapes in comp_inds are the same. If not the case this means
+        # the groups in controlled_by_param have different sizes, i.e. due to different
+        # number of comps for two different branches. In this case we pad the smaller
+        # groups with -1 to make them the same size.
+        lens = np.array([inds.shape[0] for inds in comp_inds])
+        max_len = np.max(lens)
+        pad = lambda x: np.pad(x, (0, max_len - x.shape[0]), constant_values=-1)
+        if not np.all(lens == max_len):
+            comp_inds = [
+                pad(inds) if inds.shape[0] < max_len else inds for inds in comp_inds
+            ]
+
         # Sorted inds are only used to infer the correct starting values.
-        param_vals = jnp.asarray(
-            [data.loc[inds, key].to_numpy() for inds in inds_of_comps]
-        )
+        indices_per_param = jnp.stack(comp_inds)
+
+        # Assign dummy param (ignored by nanmean later). This adds a new row to the
+        # `data` (which is, e.g., self.nodes). That new row has index `-1`, which does
+        # not clash with any other node index (they are in
+        # `[0, ..., num_total_comps-1]`).
+        data.loc[-1, key] = np.nan
+        param_vals = jnp.asarray([data.loc[inds, key].to_numpy() for inds in comp_inds])
 
         # Set the value which the trainable parameter should take.
         num_created_parameters = len(indices_per_param)
@@ -1099,7 +1113,7 @@ def make_trainable(
                     f"init_val must a float, list, or None, but it is a {type(init_val).__name__}."
                 )
         else:
-            new_params = jnp.mean(param_vals, axis=1)
+            new_params = jnp.nanmean(param_vals, axis=1)
         self.base.trainable_params.append({key: new_params})
         self.base.indices_set_by_trainables.append(indices_per_param)
         self.base.num_trainable_params += num_created_parameters
diff --git a/tests/test_make_trainable.py b/tests/test_make_trainable.py
index 50ece696..783461b3 100644
--- a/tests/test_make_trainable.py
+++ b/tests/test_make_trainable.py
@@ -531,3 +531,28 @@ def test_write_trainables(SimpleNet):
     # Test whether synapse view raises an error.
     with pytest.raises(AssertionError):
         net.select(edges=[0, 2, 3]).write_trainables(params)
+
+
+def test_param_sharing_w_different_group_sizes():
+    # test if make_trainable corresponds to set
+    branch1 = jx.Branch(nseg=6)
+    branch1.nodes["controlled_by_param"] = np.array([0, 0, 0, 1, 1, 2])
+    branch1.make_trainable("radius")
+    assert branch1.num_trainable_params == 3
+
+    # make trainable
+    params = branch1.get_parameters()
+    params[0]["radius"] = params[0]["radius"].at[:].set([2, 3, 4])
+    branch1.to_jax()
+    pstate = params_to_pstate(params, branch1.indices_set_by_trainables)
+    params1 = branch1.get_all_parameters(pstate, voltage_solver="jaxley.thomas")
+
+    # set
+    branch2 = jx.Branch(nseg=6)
+    branch2.set("radius", np.array([2, 2, 2, 3, 3, 4]))
+    params = branch2.get_parameters()
+    branch2.to_jax()
+    pstate = params_to_pstate(params, branch2.indices_set_by_trainables)
+    params2 = branch2.get_all_parameters(pstate, voltage_solver="jaxley.thomas")
+
+    assert np.array_equal(params1["radius"], params2["radius"], equal_nan=True)