diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 3125ceab227..52c4bed2a81 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1982,6 +1982,7 @@ class Tool( object, Dictifiable ):
                 group_errors = [ ]
                 any_group_errors = False
                 rep_index = 0
+                del group_state[:]  # Clear prepopulated defaults if repeat.min set.
                 while True:
                     rep_name = "%s_%d" % ( key, rep_index )
                     if not any( [ incoming_key.startswith(rep_name) for incoming_key in incoming.keys() ] ):
diff --git a/test/functional/tools/min_repeat.xml b/test/functional/tools/min_repeat.xml
new file mode 100644
index 00000000000..495c3834e9e
--- /dev/null
+++ b/test/functional/tools/min_repeat.xml
@@ -0,0 +1,27 @@
+<tool id="min_repeat" name="min_repeat">
+    <command>
+        cat #for $q in $queries# ${q.input} #end for# > $out_file1 ;
+        cat #for $q in $queries2# ${q.input2} #end for# > $out_file2
+    </command>
+    <inputs>
+        <repeat name="queries" title="Dataset" min="1">
+            <param name="input" type="data" label="Select" />
+        </repeat>
+        <repeat name="queries2" title="Dataset" min="1">
+            <param name="input2" type="data" label="Select" />
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+        <data name="out_file2" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="simple_line.txt"/>
+            <param name="input" value="simple_line.txt"/>
+            <param name="input2" value="simple_line_alternative.txt"/>
+            <output name="out_file1" file="simple_line_x2.txt"/>
+            <output name="out_file2" file="simple_line_alternative.txt"/>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 154f33506ae..7181a42c5ad 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -12,4 +12,5 @@
   <tool file="metadata.xml" />
   <tool file="output_order.xml" />
   <tool file="disambiguate_repeats.xml" />
+  <tool file="min_repeat.xml" />
 </toolbox>
\ No newline at end of file