The Palivizumab Outcomes Registry prospectively collected data on 19,548 subjects who received respiratory syncytial virus (RSV) prophylaxis with palivizumab during the 2000–2004 RSV seasons. We evaluated the characteristics of enrolled registry subjects with congenital heart disease (CHD) over the four RSV seasons and examined additional information on these subjects collected in the 2002–2004 seasons. The percentage of registry subjects with CHD increased from 4.8% (102/2116) in the first season to 11.4% (688/6050) in the last season. Across all four seasons, 1500 subjects with CHD were enrolled, 71% of whom had acyanotic CHD. The proportion with cyanotic CHD increased from 19.6% (20/102) in the 2000–2001 season to 37.5% (258/688) in the 2003–2004 season, while the proportion of all CHD in the registry more than doubled during this time. The cumulative RSV hospitalization rate was 1.9% among patients with CHD who received prophylaxis. Among subjects with cyanotic and acyanotic CHD, hospitalization rates were 2.6% and 1.6%, respectively. Prospective data collected in the Palivizumab Outcomes Registry provide the largest published dataset available on infants with CHD receiving palivizumab and show low hospitalization rates and use consistent with prelicensure clinical trial data and revised American Academy of Pediatrics guidelines.