It's possible the paths in the run command are not correct. Drop down the debug list (e.g. where it ways Tomcat RUN" and hit Edit configurations. Make sure all the paths in that long VM parameters dialog look correct. In particular look for -classpath option and make sure it points to bootstrap.jar in the tomcat bin directory (on my machine -classpath "D:/tomcat-5.5.9/bin/boostrap.jar".