Polycystic kidney disease (PKD) was previously diagnosed at necropsy in several pygmy hippopotami (Choeropsis liberiensis) from the Smithsonian National Zoo and Zoo Basel, suggesting a threat to the long-term viability of the captive population. We determined the incidence and demographics of PKD in the captive population historically; we tested if the condition is linked to pedigree; we investigated mode of inheritance; we examined effects of PKD on longevity; we conducted survival analysis; and we examined long-term population viability. Thirty-seven percent of 149 necropsied adult pygmy hippos were affected by PKD, and it was more common in females, controlling for the overall female-biased sex-ratio. Prevalence increased significantly with age, but most hippos were beyond their reproductive prime before developing clinical signs; thus fecundity was likely unaffected. PKD was linked to pedigree and may exhibit X-linked dominance, but further research is needed to definitively establish the mode of inheritance. PKD did not affect longevity, overall or within any age class. There was no significant correlation between inbreeding coefficient (F) and PKD, and the prevalence in wild-caught and captive-born animals was similar. Longevity for both captive-born and inbred hippos (F > 0) was significantly shorter than longevity for their wild-caught and non-inbred counterparts. Demographic projections indicated the extant population will likely experience a slow increase over time, provided there are no space constraints. We conclude that although PKD is an important cause of morbidity and mortality in pygmy hippos, the condition is not a primary concern for overall viability of the captive population.