diff --git a/ihm/dataset.py b/ihm/dataset.py
index c1504b4..3352af4 100644
--- a/ihm/dataset.py
+++ b/ihm/dataset.py
@@ -18,12 +18,16 @@ class Dataset(object):
     """
 
     _eq_keys = ['location']
+    _allow_duplicates = False
 
-    # Datasets compare equal iff they are the same class and have the
-    # same attributes
+    # Datasets compare equal iff they are the same class, have the
+    # same attributes, and allow_duplicates=False
     def _eq_vals(self):
-        return tuple([self.__class__]
-                     + [getattr(self, x) for x in self._eq_keys])
+        if self._allow_duplicates:
+            return id(self)
+        else:
+            return tuple([self.__class__]
+                         + [getattr(self, x) for x in self._eq_keys])
 
     def __eq__(self, other):
         return self._eq_vals() == other._eq_vals()
diff --git a/ihm/reader.py b/ihm/reader.py
index f2f2807..c0333cb 100644
--- a/ihm/reader.py
+++ b/ihm/reader.py
@@ -1384,6 +1384,7 @@ def __call__(self, data_type, id, details):
         f = self.sysr.datasets.get_by_id(
             id, self.type_map.get(typ, ihm.dataset.Dataset))
         f.details = details
+        f._allow_duplicates = True
 
 
 class _DatasetGroupHandler(Handler):
diff --git a/test/test_dataset.py b/test/test_dataset.py
index 43bd489..9b461c0 100644
--- a/test/test_dataset.py
+++ b/test/test_dataset.py
@@ -40,6 +40,17 @@ def test_dataset(self):
         d.parents.append(td)
         self.assertEqual(len(d.parents), 2)
 
+    def test_dataset_allow_duplicates(self):
+        """Test Dataset base class with allow_duplicates=True"""
+        loc = ihm.location.PDBLocation('1abc', version='foo', details='bar')
+        d = ihm.dataset.Dataset(loc)
+        d._allow_duplicates = True
+        self.assertEqual(d._eq_vals(), id(d))
+
+        d2 = ihm.dataset.Dataset(loc)
+        d2._allow_duplicates = True
+        self.assertNotEqual(d, d2)
+
     def test_add_primary_no_parents(self):
         """Test add_primary() method, no parents"""
         l1 = ihm.location.PDBLocation('1abc', version='foo', details='bar')
diff --git a/test/test_reader.py b/test/test_reader.py
index 7d9c14f..cf0c81a 100644
--- a/test/test_reader.py
+++ b/test/test_reader.py
@@ -971,6 +971,9 @@ def test_dataset_list_handler(self):
             self.assertEqual(d1.__class__, ihm.dataset.PDBDataset)
             self.assertEqual(d2.__class__, ihm.dataset.ComparativeModelDataset)
             self.assertEqual(d3.__class__, ihm.dataset.EMMicrographsDataset)
+            self.assertTrue(d1._allow_duplicates)
+            self.assertTrue(d2._allow_duplicates)
+            self.assertTrue(d3._allow_duplicates)
             # No specified data type - use base class
             self.assertEqual(d4.__class__, ihm.dataset.Dataset)
             self.assertIsNone(d1.details)