diff --git a/idea/src/org/jetbrains/kotlin/idea/run/JetJUnitConfigurationProducer.java b/idea/src/org/jetbrains/kotlin/idea/run/JetJUnitConfigurationProducer.java
index ba6690c25bb..480f8c8db3b 100644
--- a/idea/src/org/jetbrains/kotlin/idea/run/JetJUnitConfigurationProducer.java
+++ b/idea/src/org/jetbrains/kotlin/idea/run/JetJUnitConfigurationProducer.java
@@ -34,6 +34,7 @@ import com.intellij.psi.util.PsiTreeUtil;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.jetbrains.kotlin.asJava.LightClassUtil;
+import org.jetbrains.kotlin.idea.project.ProjectStructureUtil;
 import org.jetbrains.kotlin.idea.util.ProjectRootsUtil;
 import org.jetbrains.kotlin.psi.*;
 
@@ -65,6 +66,10 @@ public class JetJUnitConfigurationProducer extends RuntimeConfigurationProducer
 
         JetFile jetFile = (JetFile) leaf.getContainingFile();
 
+        if (ProjectStructureUtil.isJsKotlinModule(jetFile)) {
+            return null;
+        }
+
         JetNamedFunction function = PsiTreeUtil.getParentOfType(leaf, JetNamedFunction.class, false);
         if (function != null) {
             myElement = function;
diff --git a/idea/src/org/jetbrains/kotlin/idea/run/JetTestNgConfigurationProducer.java b/idea/src/org/jetbrains/kotlin/idea/run/JetTestNgConfigurationProducer.java
index ce24a1025b5..8ee7a4ec3ec 100644
--- a/idea/src/org/jetbrains/kotlin/idea/run/JetTestNgConfigurationProducer.java
+++ b/idea/src/org/jetbrains/kotlin/idea/run/JetTestNgConfigurationProducer.java
@@ -33,6 +33,7 @@ import com.theoryinpractice.testng.configuration.TestNGConfigurationProducer;
 import com.theoryinpractice.testng.util.TestNGUtil;
 import org.jetbrains.annotations.Nullable;
 import org.jetbrains.kotlin.asJava.LightClassUtil;
+import org.jetbrains.kotlin.idea.project.ProjectStructureUtil;
 import org.jetbrains.kotlin.idea.util.ProjectRootsUtil;
 import org.jetbrains.kotlin.psi.*;
 
@@ -62,6 +63,10 @@ public class JetTestNgConfigurationProducer extends TestNGConfigurationProducer
 
         JetFile jetFile = (JetFile) leaf.getContainingFile();
 
+        if (ProjectStructureUtil.isJsKotlinModule(jetFile)) {
+            return false;
+        }
+
         JetNamedFunction function = PsiTreeUtil.getParentOfType(leaf, JetNamedFunction.class, false);
         if (function != null) {
             @SuppressWarnings("unchecked")
diff --git a/idea/testData/run/InJsModule/module/src/test.kt b/idea/testData/run/InJsModule/module/src/test.kt
new file mode 100644
index 00000000000..c342c11f91a
--- /dev/null
+++ b/idea/testData/run/InJsModule/module/src/test.kt
@@ -0,0 +1,14 @@
+package q
+
+native
+class Foo {
+    // RUN:
+    fun foo(s: Array<String>) = noImpl
+}
+
+
+// RUN:
+native
+fun main(s: Array<String>) {
+    println("Top-level")
+}
\ No newline at end of file
diff --git a/idea/tests/org/jetbrains/kotlin/idea/run/RunConfigurationTest.kt b/idea/tests/org/jetbrains/kotlin/idea/run/RunConfigurationTest.kt
index ffc893697db..082879c683d 100644
--- a/idea/tests/org/jetbrains/kotlin/idea/run/RunConfigurationTest.kt
+++ b/idea/tests/org/jetbrains/kotlin/idea/run/RunConfigurationTest.kt
@@ -47,8 +47,9 @@ import com.intellij.psi.PsiComment
 import com.intellij.psi.PsiManager
 import org.jetbrains.kotlin.test.ConfigLibraryUtil
 import org.jetbrains.kotlin.psi.psiUtil.getStrictParentOfType
+import com.intellij.openapi.projectRoots.Sdk
 
-private val RUN_PREFIX = "// RUN: "
+private val RUN_PREFIX = "// RUN:"
 
 class RunConfigurationTest: CodeInsightTestCase() {
     fun getTestProject() = myProject!!
@@ -87,11 +88,19 @@ class RunConfigurationTest: CodeInsightTestCase() {
     }
 
     fun testClassesAndObjects() {
+        doTest(ConfigLibraryUtil::configureKotlinRuntime)
+    }
+
+    fun testInJsModule() {
+        doTest(ConfigLibraryUtil::configureKotlinJsRuntime)
+    }
+
+    private fun doTest(configureRuntime: (Module, Sdk) -> Unit) {
         val baseDir = getTestProject().getBaseDir()!!
         val createModuleResult = configureModule(moduleDirPath("module"), baseDir)
         val srcDir = createModuleResult.srcDir
 
-        ConfigLibraryUtil.configureKotlinRuntime(createModuleResult.module, PluginTestCaseBase.fullJdk())
+        configureRuntime(createModuleResult.module, PluginTestCaseBase.fullJdk())
 
         try {
             val expectedClasses = ArrayList<String>()
@@ -99,13 +108,14 @@ class RunConfigurationTest: CodeInsightTestCase() {
 
             val testFile = PsiManager.getInstance(getTestProject()).findFile(srcDir.findFileByRelativePath("test.kt"))
             testFile.accept(
-                    object: JetTreeVisitorVoid() {
+                    object : JetTreeVisitorVoid() {
                         override fun visitComment(comment: PsiComment) {
                             val declaration = comment.getStrictParentOfType<JetNamedDeclaration>()!!
                             val text = comment.getText() ?: return
                             if (!text.startsWith(RUN_PREFIX)) return
 
-                            expectedClasses.add(text.substring(RUN_PREFIX.length()).trim())
+                            val expectedClass = text.substring(RUN_PREFIX.length()).trim()
+                            if (expectedClass.isNotEmpty()) expectedClasses.add(expectedClass)
 
                             val dataContext = MapDataContext()
                             dataContext.put(Location.DATA_KEY, PsiLocation(getTestProject(), declaration))
diff --git a/idea/tests/org/jetbrains/kotlin/test/ConfigLibraryUtil.java b/idea/tests/org/jetbrains/kotlin/test/ConfigLibraryUtil.java
index b30ec83243c..358d9133e3b 100644
--- a/idea/tests/org/jetbrains/kotlin/test/ConfigLibraryUtil.java
+++ b/idea/tests/org/jetbrains/kotlin/test/ConfigLibraryUtil.java
@@ -26,27 +26,34 @@ import com.intellij.openapi.roots.ui.configuration.libraryEditor.NewLibraryEdito
 import com.intellij.openapi.util.Computable;
 import com.intellij.openapi.vfs.VfsUtil;
 import org.jetbrains.annotations.NotNull;
-import org.jetbrains.kotlin.codegen.forTestCompile.ForTestCompileRuntime;
+import org.jetbrains.kotlin.utils.PathUtil;
+
+import java.io.File;
 
 /**
  * Helper for configuring kotlin runtime in tested project.
  */
 public class ConfigLibraryUtil {
     private static final String DEFAULT_JAVA_RUNTIME_LIB_NAME = "JAVA_RUNTIME_LIB_NAME";
+    private static final String DEFAULT_KOTLIN_JS_STDLIB_NAME = "KOTLIN_JS_STDLIB_NAME";
 
     private ConfigLibraryUtil() {
     }
 
-    private static NewLibraryEditor getKotlinRuntimeLibEditor(String libName) {
+    private static NewLibraryEditor getKotlinRuntimeLibEditor(String libName, File library) {
         NewLibraryEditor editor = new NewLibraryEditor();
         editor.setName(libName);
-        editor.addRoot(VfsUtil.getUrlForLibraryRoot(ForTestCompileRuntime.runtimeJarForTests()), OrderRootType.CLASSES);
+        editor.addRoot(VfsUtil.getUrlForLibraryRoot(library), OrderRootType.CLASSES);
 
         return editor;
     }
 
     public static void configureKotlinRuntime(Module module, Sdk sdk) {
-        configureLibrary(module, sdk, getKotlinRuntimeLibEditor(DEFAULT_JAVA_RUNTIME_LIB_NAME));
+        configureLibrary(module, sdk, getKotlinRuntimeLibEditor(DEFAULT_JAVA_RUNTIME_LIB_NAME, PathUtil.getKotlinPathsForDistDirectory().getRuntimePath()));
+    }
+
+    public static void configureKotlinJsRuntime(Module module, Sdk sdk) {
+        configureLibrary(module, sdk, getKotlinRuntimeLibEditor(DEFAULT_KOTLIN_JS_STDLIB_NAME, PathUtil.getKotlinPathsForDistDirectory().getJsStdLibJarPath()));
     }
 
     public static void unConfigureKotlinRuntime(Module module, Sdk sdk) {