The purpose of this investigation was to analyze the burden of respiratory syncytial virus (RSV)-related hospitalizations in infants and children with congenital heart disease (CHD) over three consecutive RSV seasons. Retrospectively, all children with hemodynamically significant (HS-CHD) and not significant (HNS-CHD) CHD born between 2004 and 2008 at a tertiary care university hospital and identified by ICD-10 diagnoses were included. Data on RSV-related hospitalizations over the first three years of life covering at least three RSV seasons (November-April) were analyzed. The overall incidence of RSV-related hospitalization was 9.6 % (58/602), without a statistically significant difference between HS-CHD and HNS-CHD (7.3 % vs. 10.4 %; p = 0.258). Recommendation of palivizumab prophylaxis did not influence the RSV hospitalization rates between groups. Patients with HS-CHD and early surgery were significantly less often hospitalized due to RSV compared to those with delayed surgery (1.3 % vs. 14.3 %; p = 0.003). The median duration of hospitalization was 8.5 days (HS-CHD: 14 vs. 7 days; p = 0.003). Thirteen patients (22.4 %) were admitted to the intensive care unit (ICU), for a median of 10 days. The median age at admission was 2 months, with a significant difference between HS-CHD and HNS-CHD (6 vs. 2 months; p = 0.001). The majority (97 %) of RSV-related hospitalizations occurred before 12 months of age. Patients with HS-CHD had a significantly more severe course of RSV disease and were older at the time of hospitalization. Early surgery seemed to significantly reduce the risk of RSV hospitalization during the first RSV season.