diff --git a/src/harness/compilerRunner.ts b/src/harness/compilerRunner.ts
index d9082532cb5..e3c48e33e5c 100644
--- a/src/harness/compilerRunner.ts
+++ b/src/harness/compilerRunner.ts
@@ -151,7 +151,7 @@ class CompilerBaselineRunner extends RunnerBase {
             });
 
             it("Correct JS output for " + fileName, () => {
-                if (!ts.fileExtensionIs(lastUnit.name, "d.ts") && this.emit) {
+                if (!(units.length === 1 && ts.fileExtensionIs(lastUnit.name, "d.ts")) && this.emit) {
                     if (result.files.length === 0 && result.errors.length === 0) {
                         throw new Error("Expected at least one js file to be emitted or at least one error to be created.");
                     }
diff --git a/tests/baselines/reference/fileReferencesWithNoExtensions.js b/tests/baselines/reference/fileReferencesWithNoExtensions.js
new file mode 100644
index 00000000000..48421954c3a
--- /dev/null
+++ b/tests/baselines/reference/fileReferencesWithNoExtensions.js
@@ -0,0 +1,34 @@
+//// [tests/cases/compiler/fileReferencesWithNoExtensions.ts] ////
+
+//// [t.ts]
+/// <reference path="a"/>
+/// <reference path="b"/>
+/// <reference path="c"/>
+var a = aa;  // Check that a.ts is referenced
+var b = bb;  // Check that b.d.ts is referenced
+var c = cc;  // Check that c.ts has precedence over c.d.ts
+
+//// [a.ts]
+var aa = 1;
+
+//// [b.d.ts]
+declare var bb: number;
+
+//// [c.ts]
+var cc = 1;
+
+//// [c.d.ts]
+declare var xx: number;
+
+
+//// [a.js]
+var aa = 1;
+//// [c.js]
+var cc = 1;
+//// [t.js]
+/// <reference path="a"/>
+/// <reference path="b"/>
+/// <reference path="c"/>
+var a = aa; // Check that a.ts is referenced
+var b = bb; // Check that b.d.ts is referenced
+var c = cc; // Check that c.ts has precedence over c.d.ts
diff --git a/tests/baselines/reference/jsFileCompilationEmitBlockedCorrectly.errors.txt b/tests/baselines/reference/jsFileCompilationEmitBlockedCorrectly.errors.txt
new file mode 100644
index 00000000000..eb9e11e574b
--- /dev/null
+++ b/tests/baselines/reference/jsFileCompilationEmitBlockedCorrectly.errors.txt
@@ -0,0 +1,17 @@
+error TS5055: Cannot write file 'tests/cases/compiler/a.js' which is one of the input files.
+
+
+!!! error TS5055: Cannot write file 'tests/cases/compiler/a.js' which is one of the input files.
+==== tests/cases/compiler/a.ts (0 errors) ====
+    class c {
+    }
+    
+==== tests/cases/compiler/b.ts (0 errors) ====
+    // this should be emitted
+    class d {
+    }
+    
+==== tests/cases/compiler/a.js (0 errors) ====
+    function foo() {
+    }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/jsFileCompilationEmitBlockedCorrectly.js b/tests/baselines/reference/jsFileCompilationEmitBlockedCorrectly.js
new file mode 100644
index 00000000000..ea9c9f62b8d
--- /dev/null
+++ b/tests/baselines/reference/jsFileCompilationEmitBlockedCorrectly.js
@@ -0,0 +1,23 @@
+//// [tests/cases/compiler/jsFileCompilationEmitBlockedCorrectly.ts] ////
+
+//// [a.ts]
+class c {
+}
+
+//// [b.ts]
+// this should be emitted
+class d {
+}
+
+//// [a.js]
+function foo() {
+}
+
+
+//// [b.js]
+// this should be emitted
+var d = (function () {
+    function d() {
+    }
+    return d;
+})();
diff --git a/tests/baselines/reference/jsFileCompilationWithDeclarationEmitPathSameAsInput.js b/tests/baselines/reference/jsFileCompilationWithDeclarationEmitPathSameAsInput.js
new file mode 100644
index 00000000000..a7ba8b49985
--- /dev/null
+++ b/tests/baselines/reference/jsFileCompilationWithDeclarationEmitPathSameAsInput.js
@@ -0,0 +1,15 @@
+//// [tests/cases/compiler/jsFileCompilationWithDeclarationEmitPathSameAsInput.ts] ////
+
+//// [a.ts]
+class c {
+}
+
+//// [a.d.ts]
+declare function isC(): boolean;
+
+//// [a.js]
+var c = (function () {
+    function c() {
+    }
+    return c;
+})();
diff --git a/tests/baselines/reference/jsFileCompilationWithOutDeclarationFileNameSameAsInputJsFile.js b/tests/baselines/reference/jsFileCompilationWithOutDeclarationFileNameSameAsInputJsFile.js
new file mode 100644
index 00000000000..d3b2f788d66
--- /dev/null
+++ b/tests/baselines/reference/jsFileCompilationWithOutDeclarationFileNameSameAsInputJsFile.js
@@ -0,0 +1,15 @@
+//// [tests/cases/compiler/jsFileCompilationWithOutDeclarationFileNameSameAsInputJsFile.ts] ////
+
+//// [a.ts]
+class c {
+}
+
+//// [b.d.ts]
+declare function foo(): boolean;
+
+//// [b.js]
+var c = (function () {
+    function c() {
+    }
+    return c;
+})();
diff --git a/tests/cases/compiler/jsFileCompilationEmitBlockedCorrectly.ts b/tests/cases/compiler/jsFileCompilationEmitBlockedCorrectly.ts
new file mode 100644
index 00000000000..80f9358fb7f
--- /dev/null
+++ b/tests/cases/compiler/jsFileCompilationEmitBlockedCorrectly.ts
@@ -0,0 +1,13 @@
+// @jsExtensions: js
+// @filename: a.ts
+class c {
+}
+
+// @filename: b.ts
+// this should be emitted
+class d {
+}
+
+// @filename: a.js
+function foo() {
+}