Pepsinogen, the precursors of pepsin, is classified into two subtypes: pepsinogen I (PG I) and pepsinogen II (PG II). Patients with impaired renal function are associated with elevated concentrations of serum pepsinogen. Contradictory results have been reported about the effect of dialysis on the serum pepsinogen levels, as the previous studies were conducted only in a particular period of dialysis. We therefore investigated the effect of continuous ambulatory peritoneal dialysis (CAPD) or hemodialysis on serum pepsinogen levels in patients with chronic renal failure (CRF) before and after dialysis treatment. Thirty-four patients with CRF were enrolled in this study and were treated by CAPD (n = 22) or hemodialysis (n = 12). As a control group, subjects with normal renal function were included (n = 20). Serum PG I and PG II levels were measured in control subjects and CRF patients before dialysis treatment and after three-month dialysis treatment. Before dialysis treatment, serum PG I levels were significantly higher in CRF patients than control subjects. In patients treated by CAPD, the serum PG I levels were significantly decreased but its levels were still higher than the values of the control subjects, whereas PG I levels remained unchanged in patients treated by hemodialysis. There were no differences in serum PG II levels between control subjects and CRF patients before or after dialysis treatment. Thus, CAPD is more effective than hemodialysis in the clearance of PG I.