diff --git a/ide-compiler-runner/src/org/jetbrains/kotlin/modules/KotlinModuleDescriptionBuilder.java b/ide-compiler-runner/src/org/jetbrains/kotlin/modules/KotlinModuleDescriptionBuilder.java
index 29ee2814c88..f203d81809d 100644
--- a/ide-compiler-runner/src/org/jetbrains/kotlin/modules/KotlinModuleDescriptionBuilder.java
+++ b/ide-compiler-runner/src/org/jetbrains/kotlin/modules/KotlinModuleDescriptionBuilder.java
@@ -27,6 +27,7 @@ public interface KotlinModuleDescriptionBuilder {
             String outputDir,
             DependencyProvider dependencyProvider,
             List<File> sourceFiles,
+            List<File> javaSourceRoots,
             boolean tests,
             Set<File> directoriesToFilterOut
     );
diff --git a/ide-compiler-runner/src/org/jetbrains/kotlin/modules/KotlinModuleScriptBuilderFactory.java b/ide-compiler-runner/src/org/jetbrains/kotlin/modules/KotlinModuleScriptBuilderFactory.java
index 71e229a8a8b..d7d48e07964 100644
--- a/ide-compiler-runner/src/org/jetbrains/kotlin/modules/KotlinModuleScriptBuilderFactory.java
+++ b/ide-compiler-runner/src/org/jetbrains/kotlin/modules/KotlinModuleScriptBuilderFactory.java
@@ -56,6 +56,7 @@ public class KotlinModuleScriptBuilderFactory implements KotlinModuleDescription
                 String outputDir,
                 DependencyProvider dependencyProvider,
                 List<File> sourceFiles,
+                List<File> javaSourceRoots,
                 boolean tests,
                 final Set<File> directoriesToFilterOut
         ) {
@@ -74,7 +75,7 @@ public class KotlinModuleScriptBuilderFactory implements KotlinModuleDescription
                 script.append("        sources += \"" + toSystemIndependentName(sourceFile.getPath()) + "\"\n");
             }
 
-            dependencyProvider.processClassPath(new DependencyProcessor() {
+            DependencyProcessor processor = new DependencyProcessor() {
                 @Override
                 public void processClassPathSection(@NotNull String sectionDescription, @NotNull Collection<File> files) {
                     script.append("        // " + sectionDescription + "\n");
@@ -97,7 +98,13 @@ public class KotlinModuleScriptBuilderFactory implements KotlinModuleDescription
                         script.append("        annotationsPath += \"").append(toSystemIndependentName(file.getPath())).append("\"\n");
                     }
                 }
-            });
+            };
+
+            if (!javaSourceRoots.isEmpty()) {
+                processor.processClassPathSection("Java source roots", javaSourceRoots);
+            }
+
+            dependencyProvider.processClassPath(processor);
 
             script.append("    }\n");
             return this;
diff --git a/ide-compiler-runner/src/org/jetbrains/kotlin/modules/KotlinModuleXmlBuilderFactory.java b/ide-compiler-runner/src/org/jetbrains/kotlin/modules/KotlinModuleXmlBuilderFactory.java
index 11dd346897d..d11932c85a4 100644
--- a/ide-compiler-runner/src/org/jetbrains/kotlin/modules/KotlinModuleXmlBuilderFactory.java
+++ b/ide-compiler-runner/src/org/jetbrains/kotlin/modules/KotlinModuleXmlBuilderFactory.java
@@ -60,6 +60,7 @@ public class KotlinModuleXmlBuilderFactory implements KotlinModuleDescriptionBui
                 String outputDir,
                 DependencyProvider dependencyProvider,
                 List<File> sourceFiles,
+                List<File> javaSourceRoots,
                 boolean tests,
                 final Set<File> directoriesToFilterOut
         ) {
@@ -82,7 +83,7 @@ public class KotlinModuleXmlBuilderFactory implements KotlinModuleDescriptionBui
                 p.println("<", SOURCES, " ", PATH, "=\"", getEscapedPath(sourceFile), "\"/>");
             }
 
-            dependencyProvider.processClassPath(new DependencyProcessor() {
+            DependencyProcessor processor = new DependencyProcessor() {
                 @Override
                 public void processClassPathSection(@NotNull String sectionDescription, @NotNull Collection<File> files) {
                     p.println("<!-- ", sectionDescription, " -->");
@@ -110,10 +111,16 @@ public class KotlinModuleXmlBuilderFactory implements KotlinModuleDescriptionBui
                 public void processAnnotationRoots(@NotNull List<File> files) {
                     p.println("<!-- External annotations -->");
                     for (File file : files) {
-                        p.println("<", EXTERNAL_ANNOTATIONS, " ", PATH, "= \"", getEscapedPath(file), "\"/>");
+                        p.println("<", EXTERNAL_ANNOTATIONS, " ", PATH, "=\"", getEscapedPath(file), "\"/>");
                     }
                 }
-            });
+            };
+
+            if (!javaSourceRoots.isEmpty()) {
+                processor.processClassPathSection("Java source roots", javaSourceRoots);
+            }
+
+            dependencyProvider.processClassPath(processor);
 
             closeTag(p, MODULE);
             return this;
diff --git a/idea/testData/modules.xml/basic.xml b/idea/testData/modules.xml/basic.xml
index 340cb84d589..fff49604ea7 100644
--- a/idea/testData/modules.xml/basic.xml
+++ b/idea/testData/modules.xml/basic.xml
@@ -3,9 +3,11 @@
     <module name="name" outputDir="output">
         <sources path="s1"/>
         <sources path="s2"/>
+        <!-- Java source roots -->
+        <classpath path="java"/>
         <!-- External annotations -->
-        <externalAnnotations path= "a1/f1"/>
-        <externalAnnotations path= "a2"/>
+        <externalAnnotations path="a1/f1"/>
+        <externalAnnotations path="a2"/>
         <!-- s1 -->
         <classpath path="cp1"/>
         <classpath path="cp2"/>
diff --git a/idea/testData/modules.xml/filtered.xml b/idea/testData/modules.xml/filtered.xml
index e7ed7eb1982..945d7da1c80 100644
--- a/idea/testData/modules.xml/filtered.xml
+++ b/idea/testData/modules.xml/filtered.xml
@@ -4,8 +4,8 @@
         <sources path="s1"/>
         <sources path="s2"/>
         <!-- External annotations -->
-        <externalAnnotations path= "a1/f1"/>
-        <externalAnnotations path= "a2"/>
+        <externalAnnotations path="a1/f1"/>
+        <externalAnnotations path="a2"/>
         <!-- s1 -->
         <!-- Output directory, commented out -->
         <!-- 
diff --git a/idea/testData/modules.xml/multiple.xml b/idea/testData/modules.xml/multiple.xml
index e9e7155d60a..1d7462d9989 100644
--- a/idea/testData/modules.xml/multiple.xml
+++ b/idea/testData/modules.xml/multiple.xml
@@ -4,8 +4,8 @@
         <sources path="s1"/>
         <sources path="s2"/>
         <!-- External annotations -->
-        <externalAnnotations path= "a1/f1"/>
-        <externalAnnotations path= "a2"/>
+        <externalAnnotations path="a1/f1"/>
+        <externalAnnotations path="a2"/>
         <!-- s1 -->
         <!-- Output directory, commented out -->
         <!-- 
@@ -18,8 +18,8 @@
         <sources path="s12"/>
         <sources path="s22"/>
         <!-- External annotations -->
-        <externalAnnotations path= "a12/f12"/>
-        <externalAnnotations path= "a22"/>
+        <externalAnnotations path="a12/f12"/>
+        <externalAnnotations path="a22"/>
         <!-- s12 -->
         <!-- Output directory, commented out -->
         <!-- 
diff --git a/idea/tests/org/jetbrains/kotlin/modules/KotlinModuleXmlGeneratorTest.java b/idea/tests/org/jetbrains/kotlin/modules/KotlinModuleXmlGeneratorTest.java
index 50a2427df1d..c5045949787 100644
--- a/idea/tests/org/jetbrains/kotlin/modules/KotlinModuleXmlGeneratorTest.java
+++ b/idea/tests/org/jetbrains/kotlin/modules/KotlinModuleXmlGeneratorTest.java
@@ -37,8 +37,10 @@ public class KotlinModuleXmlGeneratorTest extends TestCase {
                     }
                 },
                 Arrays.asList(new File("s1"), new File("s2")),
+                Collections.singletonList(new File("java")),
                 false,
-                Collections.<File>emptySet()).asText().toString();
+                Collections.<File>emptySet()
+        ).asText().toString();
         JetTestUtils.assertEqualsToFile(new File("idea/testData/modules.xml/basic.xml"), actual);
     }
 
@@ -54,8 +56,10 @@ public class KotlinModuleXmlGeneratorTest extends TestCase {
                     }
                 },
                 Arrays.asList(new File("s1"), new File("s2")),
+                Collections.<File>emptyList(),
                 false,
-                Collections.singleton(new File("cp1"))).asText().toString();
+                Collections.singleton(new File("cp1"))
+        ).asText().toString();
         JetTestUtils.assertEqualsToFile(new File("idea/testData/modules.xml/filtered.xml"), actual);
     }
 
@@ -72,8 +76,10 @@ public class KotlinModuleXmlGeneratorTest extends TestCase {
                     }
                 },
                 Arrays.asList(new File("s1"), new File("s2")),
+                Collections.<File>emptyList(),
                 false,
-                Collections.singleton(new File("cp1")));
+                Collections.singleton(new File("cp1"))
+        );
         builder.addModule(
                 "name2",
                 "output2",
@@ -85,8 +91,10 @@ public class KotlinModuleXmlGeneratorTest extends TestCase {
                     }
                 },
                 Arrays.asList(new File("s12"), new File("s22")),
+                Collections.<File>emptyList(),
                 true,
-                Collections.singleton(new File("cp12")));
+                Collections.singleton(new File("cp12"))
+        );
         String actual = builder.asText().toString();
         JetTestUtils.assertEqualsToFile(new File("idea/testData/modules.xml/multiple.xml"), actual);
     }
diff --git a/jps-plugin/src/org/jetbrains/kotlin/jps/build/KotlinBuilderModuleScriptGenerator.java b/jps-plugin/src/org/jetbrains/kotlin/jps/build/KotlinBuilderModuleScriptGenerator.java
index 1da65710ab5..46b8b5828f5 100644
--- a/jps-plugin/src/org/jetbrains/kotlin/jps/build/KotlinBuilderModuleScriptGenerator.java
+++ b/jps-plugin/src/org/jetbrains/kotlin/jps/build/KotlinBuilderModuleScriptGenerator.java
@@ -89,8 +89,9 @@ public class KotlinBuilderModuleScriptGenerator {
             builder.addModule(
                     target.getId(),
                     outputDir.getAbsolutePath(),
-                    getKotlinModuleDependencies(context, target),
+                    getKotlinModuleDependencies(target),
                     moduleSources,
+                    findSourceRoots(context, target),
                     target.isTests(),
                     // this excludes the output directories from the class path, to be removed for true incremental compilation
                     outputDirs
@@ -115,12 +116,11 @@ public class KotlinBuilderModuleScriptGenerator {
         return outputDir;
     }
 
-    private static DependencyProvider getKotlinModuleDependencies(final CompileContext context, final ModuleBuildTarget target) {
+    private static DependencyProvider getKotlinModuleDependencies(final ModuleBuildTarget target) {
         return new DependencyProvider() {
             @Override
             public void processClassPath(@NotNull DependencyProcessor processor) {
                 processor.processClassPathSection("Classpath", findClassPathRoots(target));
-                processor.processClassPathSection("Java Source Roots", findSourceRoots(context, target));
                 processor.processAnnotationRoots(findAnnotationRoots(target));
             }
         };
@@ -132,9 +132,9 @@ public class KotlinBuilderModuleScriptGenerator {
     }
 
     @NotNull
-    private static Collection<File> findSourceRoots(@NotNull CompileContext context, @NotNull ModuleBuildTarget target) {
+    private static List<File> findSourceRoots(@NotNull CompileContext context, @NotNull ModuleBuildTarget target) {
         List<JavaSourceRootDescriptor> roots = context.getProjectDescriptor().getBuildRootIndex().getTargetRoots(target, context);
-        Collection<File> result = ContainerUtil.newArrayList();
+        List<File> result = ContainerUtil.newArrayList();
         for (JavaSourceRootDescriptor root : roots) {
             File file = root.getRootFile();
             if (file.exists()) {