diff --git a/spring-boot-integration-tests/spring-boot-gradle-tests/src/test/java/org/springframework/boot/gradle/MixedVersionRepackagingTests.java b/spring-boot-integration-tests/spring-boot-gradle-tests/src/test/java/org/springframework/boot/gradle/MixedVersionRepackagingTests.java
new file mode 100644
index 0000000000..394176375c
--- /dev/null
+++ b/spring-boot-integration-tests/spring-boot-gradle-tests/src/test/java/org/springframework/boot/gradle/MixedVersionRepackagingTests.java
@@ -0,0 +1,83 @@
+/*
+ * Copyright 2012-2016 the original author or authors.
+ *
+ * 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.springframework.boot.gradle;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.jar.JarFile;
+
+import org.assertj.core.api.Condition;
+import org.assertj.core.description.TextDescription;
+import org.gradle.tooling.ProjectConnection;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.assertj.core.api.Assertions.not;
+
+/**
+ * Integration tests for Gradle repackaging with two different versions of the same
+ * dependency.
+ *
+ * @author Andy Wilkinson
+ */
+public class MixedVersionRepackagingTests {
+
+	private static final String BOOT_VERSION = Versions.getBootVersion();
+
+	private static ProjectConnection project;
+
+	@BeforeClass
+	public static void createProject() throws IOException {
+		project = new ProjectCreator().createProject("mixed-version-repackaging");
+	}
+
+	@Test
+	public void singleVersionIsIncludedInJar() throws IOException {
+		project.newBuild().forTasks("clean", "build")
+				.withArguments("-PbootVersion=" + BOOT_VERSION, "-Prepackage=true",
+						"-PexcludeDevtools=false")
+				.run();
+		File buildLibs = new File("target/mixed-version-repackaging/build/libs");
+		File repackageFile = new File(buildLibs, "mixed-version-repackaging.jar");
+		assertThat(repackageFile.exists()).isTrue();
+		assertThat(new JarFile(repackageFile))
+				.has(entryNamed("BOOT-INF/lib/guava-18.0.jar"));
+		assertThat(new JarFile(repackageFile))
+				.has(not(entryNamed("BOOT-INF/lib/guava-16.0.jar")));
+	}
+
+	private Condition<JarFile> entryNamed(String name) {
+		return new JarFileEntryCondition(name);
+	}
+
+	private final class JarFileEntryCondition extends Condition<JarFile> {
+
+		private final String entryName;
+
+		private JarFileEntryCondition(String entryName) {
+			super(new TextDescription("entry named '%s'", entryName));
+			this.entryName = entryName;
+		}
+
+		@Override
+		public boolean matches(JarFile jarFile) {
+			return jarFile.getEntry(this.entryName) != null;
+		}
+	}
+
+}
diff --git a/spring-boot-integration-tests/spring-boot-gradle-tests/src/test/resources/mixed-version-repackaging.gradle b/spring-boot-integration-tests/spring-boot-gradle-tests/src/test/resources/mixed-version-repackaging.gradle
new file mode 100644
index 0000000000..9fb72c1c14
--- /dev/null
+++ b/spring-boot-integration-tests/spring-boot-gradle-tests/src/test/resources/mixed-version-repackaging.gradle
@@ -0,0 +1,30 @@
+buildscript {
+	repositories {
+		mavenLocal()
+		mavenCentral()
+	}
+	dependencies {
+		classpath "org.springframework.boot:spring-boot-gradle-plugin:${project.bootVersion}"
+	}
+}
+
+repositories {
+	mavenLocal()
+	mavenCentral()
+}
+
+apply plugin: 'spring-boot'
+apply plugin: 'java'
+
+dependencies {
+	compile 'com.google.guava:guava:16.0'
+	runtime 'com.google.guava:guava:18.0'
+}
+
+dependencyManagement {
+	overriddenByDependencies = false
+}
+
+springBoot {
+	mainClass = 'foo.bar.Baz'
+}
diff --git a/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/repackage/ProjectLibraries.java b/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/repackage/ProjectLibraries.java
index 2c82f06fd5..db01938f5f 100644
--- a/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/repackage/ProjectLibraries.java
+++ b/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/repackage/ProjectLibraries.java
@@ -87,16 +87,12 @@ class ProjectLibraries implements Libraries {
 			libraries(custom, callback);
 		}
 		else {
-			Set<GradleLibrary> compile = getLibraries("compile", LibraryScope.COMPILE);
 			Set<GradleLibrary> runtime = getLibraries("runtime", LibraryScope.RUNTIME);
-			runtime = minus(runtime, compile);
 			Set<GradleLibrary> provided = getLibraries(this.providedConfigurationName,
 					LibraryScope.PROVIDED);
 			if (provided != null) {
-				compile = minus(compile, provided);
 				runtime = minus(runtime, provided);
 			}
-			libraries(compile, callback);
 			libraries(runtime, callback);
 			libraries(provided, callback);
 		}