diff --git a/src/harness/harness.ts b/src/harness/harness.ts
index 1adf661226e..2d2c90dcb5e 100644
--- a/src/harness/harness.ts
+++ b/src/harness/harness.ts
@@ -1343,7 +1343,7 @@ namespace Harness {
 
         export function getErrorBaseline(inputFiles: ReadonlyArray<TestFile>, diagnostics: ReadonlyArray<ts.Diagnostic>, pretty?: boolean) {
             let outputLines = "";
-            const gen = iterateErrorBaseline(inputFiles, diagnostics, pretty);
+            const gen = iterateErrorBaseline(inputFiles, diagnostics, { pretty });
             for (let {done, value} = gen.next(); !done; { done, value } = gen.next()) {
                 const [, content] = value;
                 outputLines += content;
@@ -1353,7 +1353,7 @@ namespace Harness {
 
         export const diagnosticSummaryMarker = "__diagnosticSummary";
         export const globalErrorsMarker = "__globalErrors";
-        export function *iterateErrorBaseline(inputFiles: ReadonlyArray<TestFile>, diagnostics: ReadonlyArray<ts.Diagnostic>, pretty?: boolean): IterableIterator<[string, string, number]> {
+        export function *iterateErrorBaseline(inputFiles: ReadonlyArray<TestFile>, diagnostics: ReadonlyArray<ts.Diagnostic>, options?: { pretty?: boolean, caseSensitive?: boolean, currentDirectory?: string }): IterableIterator<[string, string, number]> {
             diagnostics = ts.sort(diagnostics, ts.compareDiagnostics);
             let outputLines = "";
             // Count up all errors that were found in files other than lib.d.ts so we don't miss any
@@ -1391,7 +1391,7 @@ namespace Harness {
                 }
             }
 
-            yield [diagnosticSummaryMarker, utils.removeTestPathPrefixes(minimalDiagnosticsToString(diagnostics, pretty)) + IO.newLine() + IO.newLine(), diagnostics.length];
+            yield [diagnosticSummaryMarker, utils.removeTestPathPrefixes(minimalDiagnosticsToString(diagnostics, options && options.pretty)) + IO.newLine() + IO.newLine(), diagnostics.length];
 
             // Report global errors
             const globalErrors = diagnostics.filter(err => !err.file);
@@ -1406,7 +1406,7 @@ namespace Harness {
                 // Filter down to the errors in the file
                 const fileErrors = diagnostics.filter((e): e is ts.DiagnosticWithLocation => {
                     const errFn = e.file;
-                    return !!errFn && utils.removeTestPathPrefixes(errFn.fileName) === utils.removeTestPathPrefixes(inputFile.unitName);
+                    return !!errFn && ts.comparePaths(utils.removeTestPathPrefixes(errFn.fileName), utils.removeTestPathPrefixes(inputFile.unitName), options && options.currentDirectory || "", !(options && options.caseSensitive)) === ts.Comparison.EqualTo;
                 });
 
 
diff --git a/src/harness/rwcRunner.ts b/src/harness/rwcRunner.ts
index 72a372036cc..e86a8d01f70 100644
--- a/src/harness/rwcRunner.ts
+++ b/src/harness/rwcRunner.ts
@@ -35,6 +35,7 @@ namespace RWC {
             const baseName = ts.getBaseFileName(jsonPath);
             let currentDirectory: string;
             let useCustomLibraryFile: boolean;
+            let caseSensitive: boolean;
             after(() => {
                 // Mocha holds onto the closure environment of the describe callback even after the test is done.
                 // Therefore we have to clean out large objects after the test is done.
@@ -47,7 +48,8 @@ namespace RWC {
                 // useCustomLibraryFile is a flag specified in the json object to indicate whether to use built/local/lib.d.ts
                 // or to use lib.d.ts inside the json object. If the flag is true, use the lib.d.ts inside json file
                 // otherwise use the lib.d.ts from built/local
-                useCustomLibraryFile = undefined!;
+                useCustomLibraryFile = false;
+                caseSensitive = false;
             });
 
             it("can compile", function(this: Mocha.ITestCallbackContext) {
@@ -93,7 +95,7 @@ namespace RWC {
                         if (!uniqueNames.has(normalized)) {
                             uniqueNames.set(normalized, true);
                             // Load the file
-                            inputFiles.push(getHarnessCompilerInputUnit(normalized));
+                            inputFiles.push(getHarnessCompilerInputUnit(fileName));
                         }
                     }
 
@@ -102,7 +104,7 @@ namespace RWC {
                         const unitName = ts.normalizeSlashes(Harness.IO.resolvePath(fileRead.path)!);
                         if (!uniqueNames.has(unitName) && !Harness.isDefaultLibraryFile(fileRead.path)) {
                             uniqueNames.set(unitName, true);
-                            otherFiles.push(getHarnessCompilerInputUnit(unitName));
+                            otherFiles.push(getHarnessCompilerInputUnit(fileRead.path));
                         }
                         else if (!opts.options.noLib && Harness.isDefaultLibraryFile(fileRead.path) && !uniqueNames.has(unitName) && useCustomLibraryFile) {
                             // If useCustomLibraryFile is true, we will use lib.d.ts from json object
@@ -111,7 +113,7 @@ namespace RWC {
                             // lib.d.ts inside json file. However, some RWC cases will still use
                             // their own version of lib.d.ts because they have customized lib.d.ts
                             uniqueNames.set(unitName, true);
-                            inputFiles.push(getHarnessCompilerInputUnit(unitName));
+                            inputFiles.push(getHarnessCompilerInputUnit(fileRead.path));
                         }
                     }
                 });
@@ -122,11 +124,12 @@ namespace RWC {
                     opts.options.noLib = true;
                 }
 
+                caseSensitive = ioLog.useCaseSensitiveFileNames || false;
                 // Emit the results
                 compilerResult = Harness.Compiler.compileFiles(
                     inputFiles,
                     otherFiles,
-                    { useCaseSensitiveFileNames: "" + (ioLog.useCaseSensitiveFileNames || false) },
+                    { useCaseSensitiveFileNames: "" + caseSensitive },
                     opts.options,
                     // Since each RWC json file specifies its current directory in its json file, we need
                     // to pass this information in explicitly instead of acquiring it from the process.
@@ -182,7 +185,7 @@ namespace RWC {
                     // Do not include the library in the baselines to avoid noise
                     const baselineFiles = tsconfigFiles.concat(inputFiles, otherFiles).filter(f => !Harness.isDefaultLibraryFile(f.unitName));
                     const errors = compilerResult.diagnostics.filter(e => !e.file || !Harness.isDefaultLibraryFile(e.file.fileName));
-                    return Harness.Compiler.iterateErrorBaseline(baselineFiles, errors);
+                    return Harness.Compiler.iterateErrorBaseline(baselineFiles, errors, { caseSensitive, currentDirectory });
                 }, baselineOpts);
             });
 
@@ -202,7 +205,7 @@ namespace RWC {
                         compilerResult = undefined!;
                         const declFileCompilationResult = Harness.Compiler.compileDeclarationFiles(declContext)!;
 
-                        return Harness.Compiler.iterateErrorBaseline(tsconfigFiles.concat(declFileCompilationResult.declInputFiles, declFileCompilationResult.declOtherFiles), declFileCompilationResult.declResult.diagnostics);
+                        return Harness.Compiler.iterateErrorBaseline(tsconfigFiles.concat(declFileCompilationResult.declInputFiles, declFileCompilationResult.declOtherFiles), declFileCompilationResult.declResult.diagnostics, { caseSensitive, currentDirectory });
                     }, baselineOpts);
                 }
             });