Center differences in short-term survival after heart transplant (HT) are known. We sought to compare long-term graft survival (freedom from death or retransplantation) at currently active United States HT centers stratified by performance for short-term survival. We used the Organ Procurement and Transplant Network database to identify subjects ≥18 years old who received primary HT during 2000 to 2014 at US centers active during 2013 and 2014. Follow-up was available until March 2016. Center case-mix was assessed by computing expected 90-day mortality and short-term performance by 90-day standardized mortality ratio (SMR; observed/expected mortality). Centers were stratified by case-mix as transplanting low-, intermediate-, and high-risk patients and by short-term performance as SMR quintiles. Center-level differences in long-term graft survival were assessed by risk-adjusted, mixed-effects Weibull survival models with center as a random effect. We analyzed 25 467 HT recipients at 96 centers. Those receiving HT at centers with superior (lower) 90-day SMR had longer graft survival (P for trend <0.001). Survival difference among SMR groups remained significant in 90-day conditional survivors (P for trend <0.001). There was significant center-level variation in risk-adjusted graft survival censored at 5 years (P<0.001) and with all follow-up (P<0.001). Adjusting for 90-day SMR was associated with 62% reduction in center variation in 5-year graft survival and 56% reduction in center variation in overall graft survival. HT recipients at centers with superior short-term outcomes have longer graft survival on long-term follow-up. Allocating resources to improve patient care processes and transplant expertise at high-SMR centers may improve short-term and overall survival after HT.