diff --git a/src/compiler/program.ts b/src/compiler/program.ts
index 9b52b8dc9ca..ecd8fd71f88 100644
--- a/src/compiler/program.ts
+++ b/src/compiler/program.ts
@@ -176,7 +176,7 @@ module ts {
             }
             var diagnostic: DiagnosticMessage;
             if (hasExtension(filename)) {
-                if (!options.allowNonTsExtensions && !fileExtensionIs(filename, ".ts")) {
+                if (!options.allowNonTsExtensions && !fileExtensionIs(host.getCanonicalFileName(filename), ".ts")) {
                     diagnostic = Diagnostics.File_0_must_have_extension_ts_or_d_ts;
                 }
                 else if (!findSourceFile(filename, isDefaultLib, refFile, refPos, refEnd)) {