diff --git a/src/fsharp/fsc.fs b/src/fsharp/fsc.fs
index 8afb5e29a0..57aa4a9d94 100755
--- a/src/fsharp/fsc.fs
+++ b/src/fsharp/fsc.fs
@@ -1771,6 +1771,38 @@ let main0(ctok, argv, referenceResolver, bannerAlreadyPrinted, openBinariesInMem
         with e -> 
             errorRecoveryNoRange e
             exiter.Exit 1
+    
+    let inputs =
+        // Deduplicate module names
+        let seen = Dictionary<string,Set<string>>()
+        let deduplicate (paths: Set<string>) path (qualifiedNameOfFile: QualifiedNameOfFile) =
+            let count = if paths.Contains path then paths.Count else paths.Count + 1
+            seen.[qualifiedNameOfFile.Text] <- Set.add path paths
+            let id = qualifiedNameOfFile.Id
+            if count = 1 then qualifiedNameOfFile else QualifiedNameOfFile(Ident(id.idText + "___" + count.ToString(),id.idRange))
+        inputs
+        |> List.map (fun (input,x) -> 
+            match input with
+            | ParsedInput.ImplFile (ParsedImplFileInput.ParsedImplFileInput(fileName,isScript,qualifiedNameOfFile,scopedPragmas,hashDirectives,modules,(isLastCompiland,isExe))) ->
+                let path = Path.GetDirectoryName fileName
+                match seen.TryGetValue qualifiedNameOfFile.Text with
+                | true, paths ->
+                    let qualifiedNameOfFile = deduplicate paths path qualifiedNameOfFile
+                    let input = ParsedInput.ImplFile(ParsedImplFileInput.ParsedImplFileInput(fileName,isScript,qualifiedNameOfFile,scopedPragmas,hashDirectives,modules,(isLastCompiland,isExe)))
+                    input,x
+                | _ ->
+                    seen.Add(qualifiedNameOfFile.Text,Set.singleton path)
+                    input,x
+            | ParsedInput.SigFile (ParsedSigFileInput.ParsedSigFileInput(fileName,qualifiedNameOfFile,scopedPragmas,hashDirectives,modules)) ->
+                let path = Path.GetDirectoryName fileName
+                match seen.TryGetValue qualifiedNameOfFile.Text with
+                | true, paths ->
+                    let qualifiedNameOfFile = deduplicate paths path qualifiedNameOfFile
+                    let input = ParsedInput.SigFile (ParsedSigFileInput.ParsedSigFileInput(fileName,qualifiedNameOfFile,scopedPragmas,hashDirectives,modules))
+                    input,x
+                | _ ->
+                    seen.Add(qualifiedNameOfFile.Text,Set.singleton path)
+                    input,x)
 
     if tcConfig.parseOnly then exiter.Exit 0 
     if not tcConfig.continueAfterParseFailure then