BACKGROUND Post-transplant survival in pediatric heart transplant (HT) recipients has improved for recent era recipients. However, the era effect has not been assessed after adjusting for baseline risk factors in HT recipients. METHODS We compared baseline characteristics and 5-year survival in pediatric HT recipients in three eras (early: July 1994 to June 1997, n = 1,153; middle: July 1997 to June 2000, n = 1,085; recent: July 2000 to June 2003, n = 1,138) for all recipients <18 years of age who were reported to the registry of the International Society for Heart and Lung Transplantation (n = 3,376). We used a Cox proportional hazards model for determining risk-adjusted era effect on death or graft loss (retransplant). RESULTS There were more retransplants and more recipients had pre-formed antibodies in the recent eras. Recent era recipients were more likely to be supported by inotropes, ventilator, mechanical support and dialysis at the time of transplant. Five-year survival was better for patients who underwent HT in the middle era (hazard ratio [HR] 0.79, 95% confidence interval [CI] 0.68 to 0.93, p = 0.003) and the recent era (HR 0.70, CI 0.60 to 0.82, p < 0.001) as compared with those in the early era, adjusted for baseline risk factors. The determinants of conditional 5-year survival in HT recipients who survived the first 6 months were recipient and donor age, recipient gender, retransplant, pre-formed antibodies and inotropes, but not transplant era. CONCLUSIONS Despite the worse baseline risk profile of pediatric HT recipients in recent years, their risk-adjusted survival during the first 5 years after transplant has improved. The entire era effect appears to be due to improved survival during the first 6 months post-transplant.