Background: Polycystic kidney disease (PCKD) is one of the most common inherited disorders in end-stage renal disease patients. It is generally thought that the survival of PCKD patients undergoing dialysis surpasses that of general dialysis patients, but the cause of this improved survival is not clear. Methods: Using Taiwan's national health insurance claims data, we performed a longitudinal cohort study to investigate the survival and impact of comorbidities on mortality in dialysis patients with and without PCKD. We excluded patients without diabetes mellitus (DM) in a further analysis. A Cox proportional hazards model was used to identify the risk factors for allcause mortality. The Kaplan-Meier method was used to describe overall patient survival. Results: Five hundred and one (2.25%) of 22,298 nondiabetic incident dialysis patients had PCKD. We found no significant difference in survival rates between those with and without PCKD. Being male, being over 65 years old and having congestive heart failure or cerebrovascular accident were each found to be independent predictors of mortality in the PCKD dialysis patients. Conclusions: Taiwan has a lower incidence rate of PCKD than Western countries. In Taiwan, there is little difference in the long-term survival between dialysis patients with and without PCKD.