The method involves filling an arterial line (42) and venous line (44) with dialysate. The arterial line and venous line are connected to a patient (50). The dialysate are pumped by a dialysate pump (22) through a dialysate membrane (31) in the arterial line and venous line, until patient blood is no more present in the arterial line and venous line. The dialysate is heated by a dialysate flow heater (47) to a target temperature during the dialysate filling. The dialysate is pumped by the dialysate pump to a dialysate chamber (29).