An extracorporeal therapy system includes: (i) a dialysis fluid circuit including dialysis fluid preparation structure to prepare a dialysis fluid for treatment, the dialysis fluid circuit including a fresh dialysis fluid pump, a used dialysis fluid pump, and at least one filter for purifying the dialysis fluid; (ii) a blood circuit including a blood filter for use during the treatment; (iii) a blood pump operable to pump blood through the blood circuit and blood filter; (iv) a source of disinfecting fluid; and (v) a control unit operable with the dialysis fluid preparation structure and the blood pump, the control unit programmed to cause the disinfecting fluid to be delivered to and located for a duration at an area of the dialysis fluid circuit having the at least one purifying filter, and wherein during the duration the disinfecting fluid is precluded from contacting at least the fresh dialysis fluid pump.