The present invention provides automated peritoneal dialysis systems, methods of operating the systems and devices for performing same. A typical therapy performed by the present invention begins by draining dialysis solution that is already in the patient's peritoneal cavity. The system pumps fresh dialysate from one of a plurality of supply bags, through an in-line heater to the patient's peritoneal cavity. After a dwell period, the spent dialysate in the cavity is pumped out of the patient to a drain or other disposal means. The system then pumps fresh dialysate from the supply bags to the patient and the procedure is repeated as defined in the therapy protocol. The system can pump a last bag of dialysate to the peritoneal cavity for an extended dwell, such as a daytime dwell.