Polycystic kidney disease (PCKD) is the most common hereditary cause of end-stage renal disease, the complications of which may prevent the choice of peritoneal dialysis (PD). The aim of this study was to explore the effects of dialysis modality on outcomes in patients with PCKD. We extracted a cohort of 1417 adult patients with PCKD initiating long-term dialysis therapy in 1999-2010 from the Taiwan National Health Insurance Research Database, among which 125 patients chose PD. The patients on HD were older and had a higher comorbidity index compared to those on PD. We compared the risks for death, hospitalization and medical expenditures between the patients on PD and propensity-score matched patients on hemodialysis (HD). The overall survival did not differ between the patients on PD and HD. The patients on PD tended to have higher hazard ratios (HR) for the first episode of hospitalization (adjusted HR 1.34 [95% CI, 1.04-1.79]). The annual medical expenses were 10% lower for the patients on PD. PD is an equivalent choice of renal replacement therapy to HD for patients with PCKD in terms of survival. Although the patients on PD had a higher risk for hospitalization, the medical expenditure for PD was 10% lower.