diff --git a/build-tools/core/src/org/jetbrains/jet/buildtools/core/BytecodeCompiler.java b/build-tools/core/src/org/jetbrains/jet/buildtools/core/BytecodeCompiler.java
index 7ff11568d09..2acaf470116 100644
--- a/build-tools/core/src/org/jetbrains/jet/buildtools/core/BytecodeCompiler.java
+++ b/build-tools/core/src/org/jetbrains/jet/buildtools/core/BytecodeCompiler.java
@@ -31,9 +31,9 @@ import org.jetbrains.jet.cli.common.messages.MessageCollectorPlainTextToStream;
 import org.jetbrains.jet.cli.jvm.JVMConfigurationKeys;
 import org.jetbrains.jet.cli.jvm.K2JVMCompiler;
 import org.jetbrains.jet.cli.jvm.compiler.CompileEnvironmentException;
+import org.jetbrains.jet.cli.jvm.compiler.CompileEnvironmentUtil;
 import org.jetbrains.jet.cli.jvm.compiler.JetCoreEnvironment;
 import org.jetbrains.jet.cli.jvm.compiler.KotlinToJVMBytecodeCompiler;
-import org.jetbrains.jet.config.CommonConfigurationKeys;
 import org.jetbrains.jet.config.CompilerConfiguration;
 import org.jetbrains.jet.utils.KotlinPaths;
 import org.jetbrains.jet.utils.KotlinPathsFromHomeDir;
@@ -59,6 +59,8 @@ public class BytecodeCompiler {
     ) {
         KotlinPaths paths = getKotlinPathsForAntTask();
         CompilerConfiguration configuration = new CompilerConfiguration();
+        configuration.put(CLIConfigurationKeys.MESSAGE_COLLECTOR_KEY, MessageCollectorPlainTextToStream.PLAIN_TEXT_TO_SYSTEM_ERR);
+
         configuration.addAll(CLASSPATH_KEY, PathUtil.getJdkClassesRoots());
         if ((stdlib != null) && (stdlib.trim().length() > 0)) {
             configuration.add(CLASSPATH_KEY, new File(stdlib));
@@ -84,14 +86,13 @@ public class BytecodeCompiler {
             configuration.add(ANNOTATIONS_PATH_KEY, jdkAnnotationsPath);
         }
 
-        configuration.addAll(CommonConfigurationKeys.SOURCE_ROOTS_KEY, Arrays.asList(sourceRoots));
+        CompileEnvironmentUtil.addSourceFilesCheckingForDuplicates(configuration, Arrays.asList(sourceRoots));
         for (String sourceRoot : sourceRoots) {
             File file = new File(sourceRoot);
             if (!file.isFile() || !"kt".equals(FileUtilRt.getExtension(file.getName()))) {
                 configuration.add(JVMConfigurationKeys.CLASSPATH_KEY, file);
             }
         }
-        configuration.put(CLIConfigurationKeys.MESSAGE_COLLECTOR_KEY, MessageCollectorPlainTextToStream.PLAIN_TEXT_TO_SYSTEM_ERR);
 
         // TODO: use K2JVMCompiler directly, don't duplicate this code here
         K2JVMCompilerArguments arguments = new K2JVMCompilerArguments();
diff --git a/compiler/cli/src/org/jetbrains/jet/cli/js/K2JSCompiler.java b/compiler/cli/src/org/jetbrains/jet/cli/js/K2JSCompiler.java
index 466a85b7a14..502fc5bc735 100644
--- a/compiler/cli/src/org/jetbrains/jet/cli/js/K2JSCompiler.java
+++ b/compiler/cli/src/org/jetbrains/jet/cli/js/K2JSCompiler.java
@@ -31,6 +31,7 @@ import org.jetbrains.annotations.Nullable;
 import org.jetbrains.jet.OutputFileCollection;
 import org.jetbrains.jet.analyzer.AnalyzeExhaust;
 import org.jetbrains.jet.cli.common.CLICompiler;
+import org.jetbrains.jet.cli.common.CLIConfigurationKeys;
 import org.jetbrains.jet.cli.common.ExitCode;
 import org.jetbrains.jet.cli.common.arguments.K2JSCompilerArguments;
 import org.jetbrains.jet.cli.common.arguments.K2JsArgumentConstants;
@@ -39,6 +40,7 @@ import org.jetbrains.jet.cli.common.messages.CompilerMessageLocation;
 import org.jetbrains.jet.cli.common.messages.CompilerMessageSeverity;
 import org.jetbrains.jet.cli.common.messages.MessageCollector;
 import org.jetbrains.jet.cli.common.output.outputUtils.OutputUtilsPackage;
+import org.jetbrains.jet.cli.jvm.compiler.CompileEnvironmentUtil;
 import org.jetbrains.jet.cli.jvm.compiler.JetCoreEnvironment;
 import org.jetbrains.jet.config.CommonConfigurationKeys;
 import org.jetbrains.jet.config.CompilerConfiguration;
@@ -84,7 +86,9 @@ public class K2JSCompiler extends CLICompiler<K2JSCompilerArguments> {
         }
 
         CompilerConfiguration configuration = new CompilerConfiguration();
-        configuration.addAll(CommonConfigurationKeys.SOURCE_ROOTS_KEY, arguments.freeArgs);
+        configuration.put(CLIConfigurationKeys.MESSAGE_COLLECTOR_KEY, messageCollector);
+
+        CompileEnvironmentUtil.addSourceFilesCheckingForDuplicates(configuration, arguments.freeArgs);
         JetCoreEnvironment environmentForJS = JetCoreEnvironment.createForProduction(rootDisposable, configuration);
 
         Project project = environmentForJS.getProject();
diff --git a/compiler/cli/src/org/jetbrains/jet/cli/jvm/K2JVMCompiler.java b/compiler/cli/src/org/jetbrains/jet/cli/jvm/K2JVMCompiler.java
index 17c10f5fb0d..696ca5d25f2 100644
--- a/compiler/cli/src/org/jetbrains/jet/cli/jvm/K2JVMCompiler.java
+++ b/compiler/cli/src/org/jetbrains/jet/cli/jvm/K2JVMCompiler.java
@@ -71,6 +71,7 @@ public class K2JVMCompiler extends CLICompiler<K2JVMCompilerArguments> {
                                 "Using Kotlin home directory " + paths.getHomePath(), CompilerMessageLocation.NO_LOCATION);
 
         CompilerConfiguration configuration = new CompilerConfiguration();
+        configuration.put(CLIConfigurationKeys.MESSAGE_COLLECTOR_KEY, messageCollector);
 
         IncrementalCacheProvider incrementalCacheProvider = (IncrementalCacheProvider) services.get(IncrementalCacheProvider.class);
         if (incrementalCacheProvider != null) {
@@ -105,7 +106,7 @@ public class K2JVMCompiler extends CLICompiler<K2JVMCompilerArguments> {
             configuration.add(CommonConfigurationKeys.SOURCE_ROOTS_KEY, arguments.freeArgs.get(0));
         }
         else {
-            configuration.addAll(CommonConfigurationKeys.SOURCE_ROOTS_KEY, arguments.freeArgs);
+            CompileEnvironmentUtil.addSourceFilesCheckingForDuplicates(configuration, arguments.freeArgs);
         }
 
         configuration.put(JVMConfigurationKeys.SCRIPT_PARAMETERS, arguments.script
@@ -114,8 +115,6 @@ public class K2JVMCompiler extends CLICompiler<K2JVMCompilerArguments> {
 
         putAdvancedOptions(configuration, arguments);
 
-        configuration.put(CLIConfigurationKeys.MESSAGE_COLLECTOR_KEY, messageCollector);
-
         messageCollector.report(CompilerMessageSeverity.LOGGING, "Configuring the compilation environment",
                                 CompilerMessageLocation.NO_LOCATION);
         try {
diff --git a/compiler/cli/src/org/jetbrains/jet/cli/jvm/compiler/CompileEnvironmentUtil.java b/compiler/cli/src/org/jetbrains/jet/cli/jvm/compiler/CompileEnvironmentUtil.java
index 56e4c1e2b4a..be7cd4c1104 100644
--- a/compiler/cli/src/org/jetbrains/jet/cli/jvm/compiler/CompileEnvironmentUtil.java
+++ b/compiler/cli/src/org/jetbrains/jet/cli/jvm/compiler/CompileEnvironmentUtil.java
@@ -17,6 +17,7 @@
 package org.jetbrains.jet.cli.jvm.compiler;
 
 import com.google.common.collect.Lists;
+import com.google.common.collect.Sets;
 import com.intellij.openapi.Disposable;
 import com.intellij.openapi.project.Project;
 import com.intellij.openapi.util.Disposer;
@@ -37,6 +38,7 @@ import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.jetbrains.jet.OutputFile;
 import org.jetbrains.jet.cli.common.CLIConfigurationKeys;
+import org.jetbrains.jet.cli.common.messages.CompilerMessageSeverity;
 import org.jetbrains.jet.cli.common.messages.MessageCollector;
 import org.jetbrains.jet.cli.common.messages.OutputMessageUtil;
 import org.jetbrains.jet.cli.common.modules.ModuleScriptData;
@@ -63,6 +65,7 @@ import java.net.URL;
 import java.net.URLClassLoader;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Set;
 import java.util.jar.*;
 
 import static org.jetbrains.jet.cli.common.messages.CompilerMessageLocation.NO_LOCATION;
@@ -272,6 +275,7 @@ public class CompileEnvironmentUtil {
     ) {
         final VirtualFileSystem localFileSystem = VirtualFileManager.getInstance().getFileSystem(StandardFileSystems.FILE_PROTOCOL);
 
+        final Set<VirtualFile> processedFiles = Sets.newHashSet();
         final List<JetFile> result = Lists.newArrayList();
 
         for (String sourceRootPath : sourceRoots) {
@@ -293,9 +297,10 @@ public class CompileEnvironmentUtil {
                 @Override
                 public Unit invoke(File file) {
                     if (file.isFile()) {
-                        VirtualFile fileByPath = localFileSystem.findFileByPath(file.getAbsolutePath());
-                        if (fileByPath != null) {
-                            PsiFile psiFile = PsiManager.getInstance(project).findFile(fileByPath);
+                        VirtualFile virtualFile = localFileSystem.findFileByPath(file.getAbsolutePath());
+                        if (virtualFile != null && !processedFiles.contains(virtualFile)) {
+                            processedFiles.add(virtualFile);
+                            PsiFile psiFile = PsiManager.getInstance(project).findFile(virtualFile);
                             if (psiFile instanceof JetFile) {
                                 result.add((JetFile) psiFile);
                             }
@@ -308,4 +313,23 @@ public class CompileEnvironmentUtil {
 
         return result;
     }
+
+    public static void addSourceFilesCheckingForDuplicates(@NotNull CompilerConfiguration configuration, @NotNull List<String> sourceRoots) {
+        MessageCollector messageCollector = configuration.get(CLIConfigurationKeys.MESSAGE_COLLECTOR_KEY);
+        assert messageCollector != null : "messageCollector should be set: " + configuration;
+
+        Set<String> uniqueSourceRoots = Sets.newLinkedHashSet();
+
+        for (String sourceRoot : sourceRoots) {
+            if (!uniqueSourceRoots.add(sourceRoot)) {
+                messageCollector.report(
+                        CompilerMessageSeverity.WARNING,
+                        "Duplicate source roots: " + sourceRoot,
+                        NO_LOCATION
+                );
+            }
+        }
+
+        configuration.put(CommonConfigurationKeys.SOURCE_ROOTS_KEY, new ArrayList<String>(uniqueSourceRoots));
+    }
 }
diff --git a/compiler/cli/src/org/jetbrains/jet/cli/jvm/compiler/KotlinToJVMBytecodeCompiler.java b/compiler/cli/src/org/jetbrains/jet/cli/jvm/compiler/KotlinToJVMBytecodeCompiler.java
index 2832ada89d5..24023f41b0a 100644
--- a/compiler/cli/src/org/jetbrains/jet/cli/jvm/compiler/KotlinToJVMBytecodeCompiler.java
+++ b/compiler/cli/src/org/jetbrains/jet/cli/jvm/compiler/KotlinToJVMBytecodeCompiler.java
@@ -19,7 +19,6 @@ package org.jetbrains.jet.cli.jvm.compiler;
 import com.google.common.base.Predicates;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
-import com.google.common.collect.Sets;
 import com.intellij.openapi.Disposable;
 import com.intellij.openapi.util.Disposer;
 import com.intellij.psi.PsiFile;
@@ -37,8 +36,6 @@ import org.jetbrains.jet.cli.common.CLIConfigurationKeys;
 import org.jetbrains.jet.cli.common.CompilerPlugin;
 import org.jetbrains.jet.cli.common.CompilerPluginContext;
 import org.jetbrains.jet.cli.common.messages.AnalyzerWithCompilerReport;
-import org.jetbrains.jet.cli.common.messages.CompilerMessageLocation;
-import org.jetbrains.jet.cli.common.messages.CompilerMessageSeverity;
 import org.jetbrains.jet.cli.common.messages.MessageCollector;
 import org.jetbrains.jet.cli.jvm.JVMConfigurationKeys;
 import org.jetbrains.jet.codegen.*;
@@ -177,29 +174,11 @@ public class KotlinToJVMBytecodeCompiler {
             configuration.add(JVMConfigurationKeys.MODULE_IDS, module.getModuleName());
         }
 
-        MessageCollector messageCollector = configuration.get(CLIConfigurationKeys.MESSAGE_COLLECTOR_KEY);
-        assert messageCollector != null : "messageCollector should be set: " + base;
-        configuration.put(CommonConfigurationKeys.SOURCE_ROOTS_KEY, checkForDuplicatePaths(messageCollector, sourceRoots));
+        CompileEnvironmentUtil.addSourceFilesCheckingForDuplicates(configuration, sourceRoots);
 
         return configuration;
     }
 
-    private static List<String> checkForDuplicatePaths(@NotNull MessageCollector messageCollector, @NotNull List<String> sourceRoots) {
-        Set<String> uniqueSourceRoots = Sets.newLinkedHashSet();
-
-        for (String sourceRoot : sourceRoots) {
-            if (!uniqueSourceRoots.add(sourceRoot)) {
-                messageCollector.report(
-                        CompilerMessageSeverity.WARNING,
-                        "Duplicate source roots: " + sourceRoot,
-                        CompilerMessageLocation.NO_LOCATION
-                );
-            }
-        }
-
-        return new ArrayList<String>(uniqueSourceRoots);
-    }
-
     @Nullable
     private static FqName findMainClass(@NotNull GenerationState generationState, @NotNull List<JetFile> files) {
         MainFunctionDetector mainFunctionDetector = new MainFunctionDetector(generationState.getBindingContext());
diff --git a/compiler/testData/cli/jvm/duplicateSource.args b/compiler/testData/cli/jvm/duplicateSource.args
deleted file mode 100644
index 5d876a0701e..00000000000
--- a/compiler/testData/cli/jvm/duplicateSource.args
+++ /dev/null
@@ -1,2 +0,0 @@
--module
-$TESTDATA_DIR$/duplicateSource.xml
diff --git a/compiler/testData/cli/jvm/duplicateSource.kt b/compiler/testData/cli/jvm/duplicateSource.kt
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/compiler/testData/cli/jvm/duplicateSource.out b/compiler/testData/cli/jvm/duplicateSource.out
deleted file mode 100644
index 6c63ae17dc9..00000000000
--- a/compiler/testData/cli/jvm/duplicateSource.out
+++ /dev/null
@@ -1,2 +0,0 @@
-WARNING: Duplicate source roots: $TESTDATA_DIR$/duplicateSource.kt
-OK
\ No newline at end of file
diff --git a/compiler/testData/cli/jvm/duplicateSource.xml b/compiler/testData/cli/jvm/duplicateSource.xml
deleted file mode 100644
index 0f352053623..00000000000
--- a/compiler/testData/cli/jvm/duplicateSource.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<modules>
-    <module name="name" outputDir="whatever">
-        <sources path="duplicateSource.kt"/>
-        <sources path="duplicateSource.kt"/>
-    </module>
-</modules>
\ No newline at end of file
diff --git a/compiler/testData/cli/jvm/duplicateSources.args b/compiler/testData/cli/jvm/duplicateSources.args
new file mode 100644
index 00000000000..bc97e01e7bc
--- /dev/null
+++ b/compiler/testData/cli/jvm/duplicateSources.args
@@ -0,0 +1,4 @@
+$TESTDATA_DIR$/simple.kt
+$TESTDATA_DIR$/simple.kt
+-d
+$TEMP_DIR$
diff --git a/compiler/testData/cli/jvm/duplicateSources.out b/compiler/testData/cli/jvm/duplicateSources.out
new file mode 100644
index 00000000000..3fa46d66e7c
--- /dev/null
+++ b/compiler/testData/cli/jvm/duplicateSources.out
@@ -0,0 +1,2 @@
+WARNING: Duplicate source roots: compiler/testData/cli/jvm/simple.kt
+OK
\ No newline at end of file
diff --git a/compiler/testData/cli/jvm/duplicateSourcesInModule.args b/compiler/testData/cli/jvm/duplicateSourcesInModule.args
new file mode 100644
index 00000000000..7f8f50de34c
--- /dev/null
+++ b/compiler/testData/cli/jvm/duplicateSourcesInModule.args
@@ -0,0 +1,2 @@
+-module
+$TESTDATA_DIR$/duplicateSourcesInModule.xml
diff --git a/compiler/testData/cli/jvm/duplicateSourcesInModule.kt b/compiler/testData/cli/jvm/duplicateSourcesInModule.kt
new file mode 100644
index 00000000000..7097ffe076a
--- /dev/null
+++ b/compiler/testData/cli/jvm/duplicateSourcesInModule.kt
@@ -0,0 +1 @@
+// this file is intentionally left blank to avoid creation of class files: this would need tuning test framework
\ No newline at end of file
diff --git a/compiler/testData/cli/jvm/duplicateSourcesInModule.out b/compiler/testData/cli/jvm/duplicateSourcesInModule.out
new file mode 100644
index 00000000000..963b2b6e862
--- /dev/null
+++ b/compiler/testData/cli/jvm/duplicateSourcesInModule.out
@@ -0,0 +1,2 @@
+WARNING: Duplicate source roots: $TESTDATA_DIR$/duplicateSourcesInModule.kt
+OK
\ No newline at end of file
diff --git a/compiler/testData/cli/jvm/duplicateSourcesInModule.xml b/compiler/testData/cli/jvm/duplicateSourcesInModule.xml
new file mode 100644
index 00000000000..dc8dadb8564
--- /dev/null
+++ b/compiler/testData/cli/jvm/duplicateSourcesInModule.xml
@@ -0,0 +1,6 @@
+<modules>
+    <module name="name" outputDir="whatever">
+        <sources path="duplicateSourcesInModule.kt"/>
+        <sources path="duplicateSourcesInModule.kt"/>
+    </module>
+</modules>
\ No newline at end of file
diff --git a/compiler/tests/org/jetbrains/jet/cli/CliCommonTest.java b/compiler/tests/org/jetbrains/jet/cli/CliCommonTest.java
index 7d3f939cfbc..c38c99afb2b 100644
--- a/compiler/tests/org/jetbrains/jet/cli/CliCommonTest.java
+++ b/compiler/tests/org/jetbrains/jet/cli/CliCommonTest.java
@@ -42,7 +42,14 @@ public class CliCommonTest extends CliBaseTest {
     }
 
     @Test
-    public void duplicateSource() throws Exception {
+    public void duplicateSources() throws Exception {
+        executeCompilerCompareOutputJVM();
+
+        Assert.assertTrue(new File(tmpdir.getTmpDir(), PackageClassUtils.getPackageClassName(FqName.ROOT) + ".class").isFile());
+    }
+
+    @Test
+    public void duplicateSourcesInModule() throws Exception {
         executeCompilerCompareOutputJVM();
     }
 
diff --git a/compiler/tests/org/jetbrains/jet/cli/KotlincExecutableTestGenerated.java b/compiler/tests/org/jetbrains/jet/cli/KotlincExecutableTestGenerated.java
index 82f931f19f1..4718a89b34a 100644
--- a/compiler/tests/org/jetbrains/jet/cli/KotlincExecutableTestGenerated.java
+++ b/compiler/tests/org/jetbrains/jet/cli/KotlincExecutableTestGenerated.java
@@ -51,9 +51,14 @@ public class KotlincExecutableTestGenerated extends AbstractKotlincExecutableTes
             doJvmTest("compiler/testData/cli/jvm/diagnosticsOrder.args");
         }
         
-        @TestMetadata("duplicateSource.args")
-        public void testDuplicateSource() throws Exception {
-            doJvmTest("compiler/testData/cli/jvm/duplicateSource.args");
+        @TestMetadata("duplicateSources.args")
+        public void testDuplicateSources() throws Exception {
+            doJvmTest("compiler/testData/cli/jvm/duplicateSources.args");
+        }
+        
+        @TestMetadata("duplicateSourcesInModule.args")
+        public void testDuplicateSourcesInModule() throws Exception {
+            doJvmTest("compiler/testData/cli/jvm/duplicateSourcesInModule.args");
         }
         
         @TestMetadata("extraHelp.args")