If you generate Hibernate classes from your database in MyEclipse, it will generate base Abstract classes for you that will be overwritten each time and concrete implementation classes that you can add any custom code to. If you were to synchronize now, your POJO would most likely be replaced by generated classes from MyEclipse that you could then build on, safely regenerating when any changes came along as long as you put your custom code in the concrete impl class and not the base abstract class. We don’t currently support partially synchronizing existing classes or the like.