Petar Tahchiev, SchemaExport does exactly what its name suggests – exports the entire schema. What version of ORM are you using? Most likely, what you want is org.hibernate.tool.hbm2ddl.SchemaUpdate, not SchemaExport.

"hibernate.hbm2ddl.auto" simply chooses between SchemaExport, SchemaUpdate, SchemaValidator, etc. when a SessionFactory is being initialized. The property doesn't affect the actual, internal operation of those tools.