diff --git a/idea/src/org/jetbrains/kotlin/idea/configuration/KotlinMavenConfigurator.java b/idea/src/org/jetbrains/kotlin/idea/configuration/KotlinMavenConfigurator.java
index e095fc154ba..ce171dce020 100644
--- a/idea/src/org/jetbrains/kotlin/idea/configuration/KotlinMavenConfigurator.java
+++ b/idea/src/org/jetbrains/kotlin/idea/configuration/KotlinMavenConfigurator.java
@@ -128,7 +128,7 @@ public abstract class KotlinMavenConfigurator implements KotlinProjectConfigurat
         if (!dialog.isOK()) return;
 
         NotificationMessageCollector collector = NotificationMessageCollectorKt.createConfigureKotlinNotificationCollector(project);
-        for (Module module : dialog.getModulesToConfigure()) {
+        for (Module module : MavenModulesRelationshipKt.excludeMavenChildrenModules(project, dialog.getModulesToConfigure())) {
             PsiFile file = findModulePomFile(module);
             if (file != null && canConfigureFile(file)) {
                 changePomFile(module, file, dialog.getKotlinVersion(), collector);
diff --git a/idea/src/org/jetbrains/kotlin/idea/configuration/MavenModulesRelationship.kt b/idea/src/org/jetbrains/kotlin/idea/configuration/MavenModulesRelationship.kt
new file mode 100644
index 00000000000..70e8f4ac4a2
--- /dev/null
+++ b/idea/src/org/jetbrains/kotlin/idea/configuration/MavenModulesRelationship.kt
@@ -0,0 +1,66 @@
+/*
+ * Copyright 2010-2016 JetBrains s.r.o.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.jetbrains.kotlin.idea.configuration
+
+import com.intellij.openapi.module.Module
+import com.intellij.openapi.project.Project
+import org.jetbrains.idea.maven.model.MavenId
+import org.jetbrains.idea.maven.project.MavenProject
+import org.jetbrains.idea.maven.project.MavenProjectsManager
+import java.util.*
+
+/**
+ * Analyze maven modules graph and exclude all children from the [selectedModules] so only
+ * topmost modules of [selectedModules] will remain.
+ *
+ * Example:
+ *
+ *
+ * - root
+ *   - module1
+ *   - module2
+ *     - module2.1
+ *     - module2.2
+ *   - module3
+ *
+ *
+ * so `excludeMavenChildrenModules(project, listOf(module2, module2.2, module1)` -> `listOf(module1, module2)`
+ *
+ */
+fun excludeMavenChildrenModules(project: Project, selectedModules: List<Module>): List<Module> {
+    val mavenManager = MavenProjectsManager.getInstance(project)
+
+    val projectsById = mavenManager.projects.associateBy { it.mavenId }
+    val selectedProjects = selectedModules.mapNotNull { mavenManager.findProject(it) }
+    val selectedIds = selectedProjects.mapTo(HashSet()) { it.mavenId }
+
+    val excluded = HashSet<MavenId>(selectedProjects.size)
+    for (m in selectedProjects) {
+        if (m.mavenId !in excluded) {
+            var current: MavenProject? = m
+            while (current != null) {
+                if (current.mavenId in excluded || (current != m && current.mavenId in selectedIds)) {
+                    excluded.add(m.mavenId)
+                    break
+                }
+                current = current.parentId?.let { projectsById[it] }
+            }
+        }
+    }
+
+    return selectedProjects.filter { it.mavenId !in excluded }.mapNotNull { mavenManager.findModule(it) }
+}