diff --git a/Jakefile.js b/Jakefile.js
index b68e869aaee..e016c1bd0bd 100644
--- a/Jakefile.js
+++ b/Jakefile.js
@@ -130,6 +130,7 @@ var harnessSources = harnessCoreSources.concat([
     "textStorage.ts",
     "moduleResolution.ts",
     "tsconfigParsing.ts",
+    "asserts.ts",
     "builder.ts",
     "commandLineParsing.ts",
     "configurationExtension.ts",
diff --git a/src/harness/harness.ts b/src/harness/harness.ts
index f4a58352b16..b38bd523fae 100644
--- a/src/harness/harness.ts
+++ b/src/harness/harness.ts
@@ -32,9 +32,30 @@
 // this will work in the browser via browserify
 var _chai: typeof chai = require("chai");
 var assert: typeof _chai.assert = _chai.assert;
-// chai's builtin `assert.isFalse` is featureful but slow - we don't use those features,
-// so we'll just overwrite it as an alterative to migrating a bunch of code off of chai
-assert.isFalse = (expr, msg) => { if (expr as any as boolean !== false) throw new Error(msg); };
+{
+    // chai's builtin `assert.isFalse` is featureful but slow - we don't use those features,
+    // so we'll just overwrite it as an alterative to migrating a bunch of code off of chai
+    assert.isFalse = (expr, msg) => { if (expr as any as boolean !== false) throw new Error(msg); };
+
+    const assertDeepImpl = assert.deepEqual;
+    assert.deepEqual = (a, b, msg) => {
+        if (ts.isArray(a) && ts.isArray(b)) {
+            assertDeepImpl(arrayExtraKeysObject(a), arrayExtraKeysObject(b), "Array extra keys differ");
+        }
+        assertDeepImpl(a, b, msg);
+
+        function arrayExtraKeysObject(a: ReadonlyArray<{} | null | undefined>): object {
+            const obj: { [key: string]: {} | null | undefined } = {};
+            for (const key in a) {
+                if (Number.isNaN(Number(key))) {
+                    obj[key] = a[key];
+                }
+            }
+            return obj;
+        }
+    };
+}
+
 declare var __dirname: string; // Node-specific
 var global: NodeJS.Global = <any>Function("return this").call(undefined);
 
diff --git a/src/harness/tsconfig.json b/src/harness/tsconfig.json
index db38b95ba6a..25642ab5179 100644
--- a/src/harness/tsconfig.json
+++ b/src/harness/tsconfig.json
@@ -108,6 +108,7 @@
         "./unittests/reuseProgramStructure.ts",
         "./unittests/moduleResolution.ts",
         "./unittests/tsconfigParsing.ts",
+        "./unittests/asserts.ts",
         "./unittests/builder.ts",
         "./unittests/commandLineParsing.ts",
         "./unittests/configurationExtension.ts",
diff --git a/src/harness/unittests/asserts.ts b/src/harness/unittests/asserts.ts
new file mode 100644
index 00000000000..ec274c44c22
--- /dev/null
+++ b/src/harness/unittests/asserts.ts
@@ -0,0 +1,11 @@
+/// <reference path="..\harness.ts" />
+
+namespace ts {
+    describe("assert", () => {
+        it("deepEqual", () => {
+            assert.throws(() => assert.deepEqual(createNodeArray([createIdentifier("A")]), createNodeArray([createIdentifier("B")])));
+            assert.throws(() => assert.deepEqual(createNodeArray([], /*hasTrailingComma*/ true), createNodeArray([], /*hasTrailingComma*/ false)));
+            assert.deepEqual(createNodeArray([createIdentifier("A")], /*hasTrailingComma*/ true), createNodeArray([createIdentifier("A")], /*hasTrailingComma*/ true));
+        });
+    });
+}
diff --git a/src/harness/unittests/reuseProgramStructure.ts b/src/harness/unittests/reuseProgramStructure.ts
index 1c0a210f442..4a76a479b18 100644
--- a/src/harness/unittests/reuseProgramStructure.ts
+++ b/src/harness/unittests/reuseProgramStructure.ts
@@ -345,7 +345,7 @@ namespace ts {
 
             const newTexts: NamedSourceText[] = files.concat([{ name: "non-existing-file.ts", text: SourceText.New("", "", `var x = 1`) }]);
             const program2 = updateProgram(program1, ["a.ts"], options, noop, newTexts);
-            assert.deepEqual(emptyArray, program2.getMissingFilePaths());
+            assert.lengthOf(program2.getMissingFilePaths(), 0);
 
             assert.equal(StructureIsReused.Not, program1.structureIsReused);
         });
@@ -839,12 +839,12 @@ namespace ts {
                     updateProgramText(files, root, "const x = 1;");
                 });
                 assert.equal(program1.structureIsReused, StructureIsReused.Completely);
-                assert.deepEqual(program2.getSemanticDiagnostics(), emptyArray);
+                assert.lengthOf(program2.getSemanticDiagnostics(), 0);
             });
 
             it("Target changes -> redirect broken", () => {
                 const program1 = createRedirectProgram();
-                assert.deepEqual(program1.getSemanticDiagnostics(), emptyArray);
+                assert.lengthOf(program1.getSemanticDiagnostics(), 0);
 
                 const program2 = updateRedirectProgram(program1, files => {
                     updateProgramText(files, axIndex, "export default class X { private x: number; private y: number; }");