A dialysis system and a method for automatically priming a dialyzer are provided. The priming of the dialyzer is accomplished in two steps; namely, the use of a blood pump to prime a dialyzer followed by the use of the blood pump and a dialysate pump to prime the dialyzer. The dialysis system filters a fluid through an extracorporeal circuit, a balanced flow loop and a dialysate loop which is connected to the dialyzer. The dialysis system and method may prevent air or air bubbles from entering the blood stream of a patient during dialysmis. Moreover, the dialysis system may be, for example, a hemodialysis or peritoneal dialysis system.