diff --git a/src/compiler/program.ts b/src/compiler/program.ts
index fb74f1dcaab33..5cb3b8dad7e8c 100644
--- a/src/compiler/program.ts
+++ b/src/compiler/program.ts
@@ -1097,7 +1097,7 @@ namespace ts {
         const modulesWithElidedImports: Map<boolean> = {};
 
         // Track source files that are JavaScript files found by searching under node_modules, as these shouldn't be compiled.
-        const jsFilesFoundSearchingNodeModules: Map<boolean> = {};
+        const sourceFilesFoundSearchingNodeModules: Map<boolean> = {};
 
         const start = new Date().getTime();
 
@@ -1378,7 +1378,7 @@ namespace ts {
                 getSourceFile: program.getSourceFile,
                 getSourceFileByPath: program.getSourceFileByPath,
                 getSourceFiles: program.getSourceFiles,
-                getFilesFromNodeModules: () => jsFilesFoundSearchingNodeModules,
+                isSourceFileFromNodeModules: (file: SourceFile) => !!lookUp(sourceFilesFoundSearchingNodeModules, file.path),
                 writeFile: writeFileCallback || (
                     (fileName, data, writeByteOrderMark, onError, sourceFiles) => host.writeFile(fileName, data, writeByteOrderMark, onError, sourceFiles)),
                 isEmitBlocked,
@@ -2066,15 +2066,17 @@ namespace ts {
                     // - noResolve is falsy
                     // - module name comes from the list of imports
                     // - it's not a top level JavaScript module that exceeded the search max
-                    const isJsFileUnderNodeModules = resolution && resolution.isExternalLibraryImport &&
-                                                 hasJavaScriptFileExtension(resolution.resolvedFileName);
+                    const isFromNodeModulesSearch = resolution && resolution.isExternalLibraryImport;
+                    const isJsFileFromNodeModules = isFromNodeModulesSearch && hasJavaScriptFileExtension(resolution.resolvedFileName);
 
-                    if (isJsFileUnderNodeModules) {
-                        jsFilesFoundSearchingNodeModules[resolvedPath] = true;
+                    if (isFromNodeModulesSearch) {
+                        sourceFilesFoundSearchingNodeModules[resolvedPath] = true;
+                    }
+                    if (isJsFileFromNodeModules) {
                         currentNodeModulesJsDepth++;
                     }
 
-                    const elideImport = isJsFileUnderNodeModules && currentNodeModulesJsDepth > maxNodeModulesJsDepth;
+                    const elideImport = isJsFileFromNodeModules && currentNodeModulesJsDepth > maxNodeModulesJsDepth;
                     const shouldAddFile = resolution && !options.noResolve && i < file.imports.length && !elideImport;
 
                     if (elideImport) {
@@ -2089,7 +2091,7 @@ namespace ts {
                                 file.imports[i].end);
                     }
 
-                    if (isJsFileUnderNodeModules) {
+                    if (isJsFileFromNodeModules) {
                         currentNodeModulesJsDepth--;
                     }
                 }
diff --git a/src/compiler/utilities.ts b/src/compiler/utilities.ts
index e8f2832cd592e..e4111e3f92563 100644
--- a/src/compiler/utilities.ts
+++ b/src/compiler/utilities.ts
@@ -36,7 +36,7 @@ namespace ts {
         getSourceFiles(): SourceFile[];
 
         /* @internal */
-        getFilesFromNodeModules(): Map<boolean>;
+        isSourceFileFromNodeModules(file: SourceFile): boolean;
 
         getCommonSourceDirectory(): string;
         getCanonicalFileName(fileName: string): string;
@@ -2277,10 +2277,9 @@ namespace ts {
         }
         else {
             const sourceFiles = targetSourceFile === undefined ? host.getSourceFiles() : [targetSourceFile];
-            const nodeModulesFiles = host.getFilesFromNodeModules();
             for (const sourceFile of sourceFiles) {
                 // Don't emit if source file is a declaration file, or was located under node_modules
-                if (!isDeclarationFile(sourceFile) && !lookUp(nodeModulesFiles, sourceFile.path)) {
+                if (!isDeclarationFile(sourceFile) && !host.isSourceFileFromNodeModules(sourceFile)) {
                     onSingleFileEmit(host, sourceFile);
                 }
             }
@@ -2314,10 +2313,9 @@ namespace ts {
         function onBundledEmit(host: EmitHost) {
             // Can emit only sources that are not declaration file and are either non module code or module with
             // --module or --target es6 specified. Files included by searching under node_modules are also not emitted.
-            const nodeModulesFiles = host.getFilesFromNodeModules();
             const bundledSources = filter(host.getSourceFiles(),
                 sourceFile => !isDeclarationFile(sourceFile) &&
-                              !lookUp(nodeModulesFiles, sourceFile.path) &&
+                              !host.isSourceFileFromNodeModules(sourceFile) &&
                               (!isExternalModule(sourceFile) ||
                                !!getEmitModuleKind(options)));
             if (bundledSources.length) {
diff --git a/tests/baselines/reference/moduleAugmentationInDependency2.js b/tests/baselines/reference/moduleAugmentationInDependency2.js
index 381f1e72d8f31..0a5d83695a34f 100644
--- a/tests/baselines/reference/moduleAugmentationInDependency2.js
+++ b/tests/baselines/reference/moduleAugmentationInDependency2.js
@@ -8,8 +8,6 @@ export {};
 //// [app.ts]
 import "A"
 
-//// [index.js]
-"use strict";
 //// [app.js]
 "use strict";
 require("A");
diff --git a/tests/baselines/reference/pathMappingBasedModuleResolution5_node.js b/tests/baselines/reference/pathMappingBasedModuleResolution5_node.js
index 1958800f91893..e4440299cc75c 100644
--- a/tests/baselines/reference/pathMappingBasedModuleResolution5_node.js
+++ b/tests/baselines/reference/pathMappingBasedModuleResolution5_node.js
@@ -31,9 +31,6 @@ exports.x = 1;
 //// [file2.js]
 "use strict";
 exports.y = 1;
-//// [file4.js]
-"use strict";
-exports.z1 = 1;
 //// [file1.js]
 "use strict";
 var file1_1 = require("folder2/file1");