diff --git a/Lib/fontTools/varLib/merger.py b/Lib/fontTools/varLib/merger.py
index 6272c4590..4ada4ba3d 100644
--- a/Lib/fontTools/varLib/merger.py
+++ b/Lib/fontTools/varLib/merger.py
@@ -713,6 +713,12 @@ class MutatorMerger(AligningMerger):
 				if gdef.MarkGlyphSetsDef is None:
 					del gdef.MarkGlyphSetsDef
 					gdef.Version = 0x00010000
+			if not (gdef.LigCaretList or
+				gdef.MarkAttachClassDef or
+				gdef.GlyphClassDef or
+				gdef.AttachList or
+				(gdef.Version >= 0x00010002 and gdef.MarkGlyphSetsDef)):
+				del font['GDEF']
 
 @MutatorMerger.merger(ot.Anchor)
 def merge(merger, self, lst):
diff --git a/Tests/varLib/data/test_results/Mutator.ttx b/Tests/varLib/data/test_results/Mutator.ttx
index 01db53043..bcedcd847 100644
--- a/Tests/varLib/data/test_results/Mutator.ttx
+++ b/Tests/varLib/data/test_results/Mutator.ttx
@@ -604,8 +604,4 @@
     </extraNames>
   </post>
 
-  <GDEF>
-    <Version value="0x00010000"/>
-  </GDEF>
-
 </ttFont>
diff --git a/Tests/varLib/data/test_results/Mutator_IUP-instance.ttx b/Tests/varLib/data/test_results/Mutator_IUP-instance.ttx
index bc6ffbf8f..8b33fd7c9 100755
--- a/Tests/varLib/data/test_results/Mutator_IUP-instance.ttx
+++ b/Tests/varLib/data/test_results/Mutator_IUP-instance.ttx
@@ -297,8 +297,4 @@
     </extraNames>
   </post>
 
-  <GDEF>
-    <Version value="0x00010000"/>
-  </GDEF>
-
 </ttFont>