Background: This study compared the lifetime costs for peritoneal dialysis (PD) and hemodialysis (HD) patients in Taiwan. Methods: Using the National Health Insurance (NHI) database of all end-stage renal disease patients on maintenance dialysis registered from July 1997 to December 2005, we matched eligible PD patients with eligible HD patients on age, sex, and diabetes status. The matched patients were followed until 31 December 2006. Patients were excluded if they were less than 18 years of age, had been diagnosed with cancer before dialysis, or had been dialyzed at centers or clinics other than hospitals. Outcomes—including life expectancy, total lifetime costs, and costs per life-year paid by the NHI—were estimated and compared. Results: The 3136 pairs of matched PD and HD patients had a mean age of 53.2 ± 15.4 years. The total lifetime cost for PD patients (US$139 360 ± US$8 336) was significantly lower than that for HD patients (US$185 235 ± US$9 623, p < 0.001). Except for patients with diabetes (who had a short life expectancy), the total lifetime cost was significantly lower for PD patients than for HD patients regardless of sex and age (p < 0.01). Conclusion: In Taiwan, the total lifetime costs paid by the NHI were lower for PD than for HD patients.