diff --git a/Orange/widgets/data/oweditdomain.py b/Orange/widgets/data/oweditdomain.py
index 567d8b5781d..a2a4b848f8c 100644
--- a/Orange/widgets/data/oweditdomain.py
+++ b/Orange/widgets/data/oweditdomain.py
@@ -680,7 +680,8 @@ class GroupItemsDialog(QDialog):
     DEFAULT_LABEL = "other"
 
     def __init__(
-            self, variable: Categorical, data: Union[np.ndarray, List],
+            self, variable: Categorical,
+            data: Union[np.ndarray, List, MArray],
             selected_attributes: List[str], dialog_settings: Dict[str, Any],
             parent: QWidget = None, flags: Qt.WindowFlags = Qt.Dialog, **kwargs
     ) -> None:
@@ -814,10 +815,18 @@ def get_merge_attributes(self) -> List[str]:
         -------
         List of attributes' to be merged names
         """
-        counts = Counter(self.data)
         if self.selected_radio.isChecked():
             return self.selected_attributes
-        elif self.n_values_radio.isChecked():
+
+        if isinstance(self.data, MArray):
+            non_nan = self.data[~self.data.mask]
+        elif isinstance(self.data, np.ndarray):
+            non_nan = self.data[~np.isnan(self.data)]
+        else:  # list
+            non_nan = [x for x in self.data if x is not None]
+
+        counts = Counter(non_nan)
+        if self.n_values_radio.isChecked():
             keep_values = self.n_values_spin.value()
             values = counts.most_common()[keep_values:]
             indices = [i for i, _ in values]
@@ -828,6 +837,8 @@ def get_merge_attributes(self) -> List[str]:
             n_all = sum(counts.values())
             indices = [v for v, c in counts.most_common()
                        if c / n_all * 100 < self.frequent_rel_spin.value()]
+
+        indices = np.array(indices, dtype=int)  # indices must be ints
         return np.array(self.variable.categories)[indices].tolist()
 
     def get_merged_value_name(self) -> str:
diff --git a/Orange/widgets/data/tests/test_oweditdomain.py b/Orange/widgets/data/tests/test_oweditdomain.py
index 4ef398bf342..e37cc5e2392 100644
--- a/Orange/widgets/data/tests/test_oweditdomain.py
+++ b/Orange/widgets/data/tests/test_oweditdomain.py
@@ -1026,6 +1026,40 @@ def test_group_keep_n(self):
         dialog.n_values_spin.setValue(3)
         self.assertListEqual(dialog.get_merge_attributes(), [])
 
+    def test_group_less_frequent_missing(self):
+        """
+        Widget gives MaskedArray to GroupItemsDialog which can have missing
+        values.
+        gh-4599
+        """
+        def _test_correctness():
+            dialog.frequent_abs_radio.setChecked(True)
+            dialog.frequent_abs_spin.setValue(3)
+            self.assertListEqual(dialog.get_merge_attributes(), ["b", "c"])
+
+            dialog.frequent_rel_radio.setChecked(True)
+            dialog.frequent_rel_spin.setValue(50)
+            self.assertListEqual(dialog.get_merge_attributes(), ["b", "c"])
+
+            dialog.n_values_radio.setChecked(True)
+            dialog.n_values_spin.setValue(1)
+            self.assertListEqual(dialog.get_merge_attributes(), ["b", "c"])
+
+        # masked array
+        data_masked = np.ma.array(
+            [0, 0, np.nan, 0, 1, 1, 2], mask=[0, 0, 1, 0, 0, 0, 0]
+        )
+        dialog = GroupItemsDialog(self.v, data_masked, [], {})
+        _test_correctness()
+
+        data_array = np.array([0, 0, np.nan, 0, 1, 1, 2])
+        dialog = GroupItemsDialog(self.v, data_array, [], {})
+        _test_correctness()
+
+        data_list = [0, 0, None, 0, 1, 1, 2]
+        dialog = GroupItemsDialog(self.v, data_list, [], {})
+        _test_correctness()
+
 
 if __name__ == '__main__':
     unittest.main()