A device for unloading compartment trays holding rod shaped elements, for use in the tobacco industry, is disclosed. The device includes an inlet conveyor for full trays, an unloading conveyor for unloading rod shaped elements into a throat, a conveyor for out-feeding stacks of rod shaped elements that have been unloaded into the throat, and an outlet conveyor for empty trays. A linear transporter for the trays has a gripping unit that grips the full trays and moves the full trays for unloading into the throat, and a second gripping unit that grips the empty trays and moves the empty trays for cleaning in a cleaning mechanism.