FULL PRODUCT VERSION : java version "1.6.0_20" Java(TM) SE Runtime Environment (build 1.6.0_20-b02) Java HotSpot(TM) Client VM (build 16.3-b01, mixed mode, sharing) ADDITIONAL OS VERSION INFORMATION : Microsoft Windows XP [version 5.1.2600] A DESCRIPTION OF THE PROBLEM : I have a resource file (named resource.txt) that is located in 2 jar files (jar1.jar and mainJar.jar). mainJar.jar depends on jar1.jar (I have a classpath entry in the manifest). When I try to load the resource from mainJar using ClassLoader.getResources() I get 2 results => GOOD Now I generate the INDEX.LIST using jar -i mainJar.jar. Running the same test again, I now have only 1 result => BAD STEPS TO FOLLOW TO REPRODUCE THE PROBLEM : Create 2 JARs with the given index in the main JAR: JarIndex-Version: 1.0 mainJarWithIndex.jar Main.class resource.txt jar1.jar resource.txt EXPECTED VERSUS ACTUAL BEHAVIOR : EXPECTED - Resource found = 2 ACTUAL - Resource found = 1 REPRODUCIBILITY : This bug can be reproduced always. ---------- BEGIN SOURCE ---------- public class Main { public static void main(String[] args) throws IOException { Enumeration<URL> e = Main.class.getClassLoader().getResources("resource.txt"); int count = 0; while (e.hasMoreElements()) { URL u = e.nextElement(); count ++; } System.out.println("Resource found = " + count); } } ---------- END SOURCE ---------- CUSTOMER SUBMITTED WORKAROUND : Do not generate INDEX.LIST but it will produce bad performances when using webstart or applet.