In my Eclipse project I'm using a third-party annotation processor, Hibernate Metamodel Generator to be exact. The annotation processor works as expected and generates files as specified by the spec. These files are generated inside the directory of the Eclipse project under a "gen" folder. In the project properties this is correctly reflected since two source folders exist - "src" and "gen." However, when the project is built for some reason all the [generated] sources under "gen" are not compiled (checking the "bin" directory I only see .class file from the "src" directory). Does anyone know why this is happening?