Background: Polycystic kidney disease (PKD) accounts for ~15% of kidney transplants but long-term outcomes in PKD kidney recipients are not well understood. Methods: In primary kidney recipients at our center (1994-2014), we compared outcomes of underlying PKD (N=619) to other native diseases (non-PKD, N=4312). Potential factors influencing outcomes in PKD were evaluated using Cox-proportional hazards regression and a rigorous multi-variable model. Results: PKD recipients were older, less likely to be sensitized, or experience delayed graft function (DGF). Over a median follow up of 5.6 years, 1256 of all recipients experienced death censored graft failure (DCGF; 115 PKD) and 1617 died (154 PKD). After adjustment for demographic, dialysis, co-morbid disease, surgical and immunologic variables, PKD recipients had a lower risk of DCGF (adjusted hazard ratio [aHR]=0.73; 95% confidence interval [CI]: 0.57-0.93; p=0.01) and death (aHR=0.62; 95% CI: 0.51-0.75; p<0.001). In our multi-adjusted model, calcineurin inhibitor (CNI) use was associated with lower risk of DCGF (aHR=0.45; 95% CI: 0.26-0.76, p=0.003), while 5-6 HLA mismatch (aHR=2.1 95% CI: 1.2-3.64, p<0.01), was associated with higher likelihood of DCGF. Notably, both pre-transplant coronary artery disease (CAD) and higher BMI were associated with increased risk of death (aHR: 2.5 for CAD [95% CI:1.69-3.71], p<0.001; aHR: 1.07 per 1 kg/m2 higher BMI [95% CI: 1.04-1.11; p<0.001), as well as, of DCGF and acute rejection. Nephrectomy at time of transplant and polycystic liver disease were not associated with DCGF/death. Incidence of post-transplant diabetes mellitus was similar between PKD and "non-PKD" cohorts. Conclusion: PKD recipients have better long-term graft and patient survival than non-PKD. Standard practices of CNI use and promoting HLA match are beneficial in PKD and should continue to be promoted. Further prospective studies investigating the potential benefits of CNI use and medical/surgical interventions to address coronary artery disease and the immunologic challenges of obesity are needed.