diff --git a/Jakefile b/Jakefile
index 6ab9155f8b3fe..767387c5d86fe 100644
--- a/Jakefile
+++ b/Jakefile
@@ -457,14 +457,16 @@ directory(builtLocalDirectory);
 var run = path.join(builtLocalDirectory, "run.js");
 compileFile(run, harnessSources, [builtLocalDirectory, tscFile].concat(libraryTargets).concat(harnessSources), [], /*useBuiltCompiler:*/ true);
 
+var internalTests = "internal/"
+
 var localBaseline = "tests/baselines/local/";
 var refBaseline = "tests/baselines/reference/";
 
-var localRwcBaseline = "tests/baselines/rwc/local/";
-var refRwcBaseline = "tests/baselines/rwc/reference/";
+var localRwcBaseline = path.join(internalTests, "baselines/rwc/local");
+var refRwcBaseline = path.join(internalTests, "baselines/rwc/reference");
 
-var localTest262Baseline = "tests/baselines/test262/local/";
-var refTest262Baseline = "tests/baselines/test262/reference/";
+var localTest262Baseline = path.join(internalTests, "baselines/test262/local");
+var refTest262Baseline = path.join(internalTests, "baselines/test262/reference");
 
 desc("Builds the test infrastructure using the built compiler");
 task("tests", ["local", run].concat(libraryTargets));
@@ -497,11 +499,13 @@ function cleanTestDirs() {
         jake.rmRf(localBaseline);
     }
 
-        // Clean the local Rwc baselines directory
+    // Clean the local Rwc baselines directory
     if (fs.existsSync(localRwcBaseline)) {
         jake.rmRf(localRwcBaseline);
     }
 
+    jake.mkdirP(localRwcBaseline);
+	jake.mkdirP(localTest262Baseline);
     jake.mkdirP(localBaseline);
 }
 
@@ -513,8 +517,8 @@ function writeTestConfigFile(tests, testConfigFile) {
 }
 
 function deleteTemporaryProjectOutput() {
-    if (fs.existsSync(localBaseline + "projectOutput/")) {
-        jake.rmRf(localBaseline + "projectOutput/");
+    if (fs.existsSync(path.join(localBaseline, "projectOutput/"))) {
+        jake.rmRf(path.join(localBaseline, "projectOutput/"));
     }
 }
 
diff --git a/src/harness/harness.ts b/src/harness/harness.ts
index a854436c5bf4d..c17a8da78e8b5 100644
--- a/src/harness/harness.ts
+++ b/src/harness/harness.ts
@@ -1569,21 +1569,32 @@ module Harness {
         export interface BaselineOptions {
             LineEndingSensitive?: boolean;
             Subfolder?: string;
+            Baselinefolder?: string;
         }
 
-        export function localPath(fileName: string, subfolder?: string) {
-            return baselinePath(fileName, 'local', subfolder);
+        export function localPath(fileName: string, baselineFolder?: string, subfolder?: string) {
+            if (baselineFolder === undefined) {
+                return baselinePath(fileName, 'local', 'tests/baselines', subfolder);
+            }
+            else {
+                return baselinePath(fileName, 'local', baselineFolder, subfolder);
+            }
         }
 
-        function referencePath(fileName: string, subfolder?: string) {
-            return baselinePath(fileName, 'reference', subfolder);
+        function referencePath(fileName: string, baselineFolder?: string, subfolder?: string) {
+            if (baselineFolder === undefined) {
+                return baselinePath(fileName, 'reference', 'tests/baselines', subfolder);
+            }
+            else {
+                return baselinePath(fileName, 'reference', baselineFolder, subfolder);
+            }
         }
 
-        function baselinePath(fileName: string, type: string, subfolder?: string) {
+        function baselinePath(fileName: string, type: string, baselineFolder: string, subfolder?: string) {
             if (subfolder !== undefined) {
-                return Harness.userSpecifiedroot + 'tests/baselines/' + subfolder + '/' + type + '/' + fileName;
+                return Harness.userSpecifiedroot + baselineFolder + '/' +  subfolder + '/' + type + '/' + fileName;
             } else {
-                return Harness.userSpecifiedroot + 'tests/baselines/' + type + '/' + fileName;
+                return Harness.userSpecifiedroot + baselineFolder + '/'  + type + '/' + fileName;
             }
         }
 
@@ -1637,7 +1648,7 @@ module Harness {
                 return;
             }
 
-            var refFileName = referencePath(relativeFileName, opts && opts.Subfolder);
+            var refFileName = referencePath(relativeFileName, opts && opts.Baselinefolder, opts && opts.Subfolder);
 
             if (actual === null) {
                 actual = '<no content>';
@@ -1675,7 +1686,7 @@ module Harness {
             opts?: BaselineOptions): void {
 
             var actual = <string>undefined;
-            var actualFileName = localPath(relativeFileName, opts && opts.Subfolder);
+            var actualFileName = localPath(relativeFileName, opts && opts.Baselinefolder, opts && opts.Subfolder);
 
             if (runImmediately) {
                 actual = generateActual(actualFileName, generateContent);
diff --git a/src/harness/rwcRunner.ts b/src/harness/rwcRunner.ts
index 3121dced76818..b66322f839021 100644
--- a/src/harness/rwcRunner.ts
+++ b/src/harness/rwcRunner.ts
@@ -26,7 +26,10 @@ module RWC {
             var otherFiles: { unitName: string; content: string; }[] = [];
             var compilerResult: Harness.Compiler.CompilerResult;
             var compilerOptions: ts.CompilerOptions;
-            var baselineOpts: Harness.Baseline.BaselineOptions = { Subfolder: 'rwc' };
+            var baselineOpts: Harness.Baseline.BaselineOptions = {
+                Subfolder: 'rwc',
+                Baselinefolder: 'internal/baselines'
+            };
             var baseName = /(.*)\/(.*).json/.exec(ts.normalizeSlashes(jsonPath))[2];
             var currentDirectory: string;
 
@@ -170,7 +173,7 @@ module RWC {
 }
 
 class RWCRunner extends RunnerBase {
-    private static sourcePath = "tests/cases/rwc/";
+    private static sourcePath = "internal/cases/rwc/";
 
     /** Setup the runner's tests so that they are ready to be executed by the harness
      *  The first test should be a describe/it block that sets up the harness's compiler instance appropriately
diff --git a/src/harness/test262Runner.ts b/src/harness/test262Runner.ts
index 24be77922f90e..0091da5e91182 100644
--- a/src/harness/test262Runner.ts
+++ b/src/harness/test262Runner.ts
@@ -3,7 +3,7 @@
 /// <reference path='syntacticCleaner.ts' />
 
 class Test262BaselineRunner extends RunnerBase {
-    private static basePath = 'tests/cases/test262';
+    private static basePath = 'internal/cases/test262';
     private static helpersFilePath = 'tests/cases/test262-harness/helpers.d.ts';
     private static helperFile = {
         unitName: Test262BaselineRunner.helpersFilePath,
@@ -15,7 +15,10 @@ class Test262BaselineRunner extends RunnerBase {
         target: ts.ScriptTarget.Latest,
         module: ts.ModuleKind.CommonJS
     };
-    private static baselineOptions: Harness.Baseline.BaselineOptions = { Subfolder: 'test262' };
+    private static baselineOptions: Harness.Baseline.BaselineOptions = {
+        Subfolder: 'test262',
+        Baselinefolder: 'internal/baselines'
+    };
 
     private static getTestFilePath(filename: string): string {
         return Test262BaselineRunner.basePath + "/" + filename;