Java: Which of multiple resources on classpath JVM takes?

If I have multiple files of the same name on classpath (e.g. I have multiple .jar with log4j.properties), what are the rules JVM follows to chose one?

It is specified by the order in which the resources (i.e. usually jar files) are specified using -classpath option. Resources 'earlier' on the classpath take precedence over resources that are specified after them. This can be also set in the manifest file of your application and then you don't need to provide -classpath option. You may want to check these articles on how to work with manifest files.

The exhaustive description of "how classes are found" can be found here, where the section on JAR-class-path Classes describes the logic of JAR-files searching.

The ClassLoader determines where a resource will be located (taken from ClassLoader JavaDoc):

The ClassLoader class uses a delegation model to search for classes and resources. Each instance of ClassLoader has an associated parent class loader. When requested to find a class or resource, a ClassLoader instance will delegate the search for the class or resource to its parent class loader before attempting to find the class or resource itself. The virtual machine's built-in class loader, called the "bootstrap class loader", does not itself have a parent but may serve as the parent of a ClassLoader instance.

So wherever in your code Class#getResource or Class#getResourceAsStream is called, this happens (taken from Class.java)

public java.net.URL getResource(String name) {
    name = resolveName(name);
    ClassLoader cl = getClassLoader0();
    if (cl==null) {
        // A system class.
        return ClassLoader.getSystemResource(name);
    }
    return cl.getResource(name);
}

ClassLoader.java:

public URL getResource(String name) {
    URL url;
    if (parent != null) {
        url = parent.getResource(name);
    } else {
        url = getBootstrapResource(name);
    }
    if (url == null) {
        url = findResource(name);
    }
    return url;
}

where ClassLoader#findResource is actually to be overwritten by the ClassLoader implementation. This implies that the behavior is different on an application server, a TomCat or if you are running from a jar file, it depends on the ClassLoader implementations of the environment you are currently in.

Here is an example that you may use to trace what's going under the hood in your particular case.