BACKGROUND: While the association of congenital heart disease (CHD) and growth retardation (GR) is known, data remain limited. This study investigated the incidence of GR and its neonatal risk factors in patients with CHD using nationwide population-based claims data. METHOD: The study population was extracted from Korean National Health Insurance Service claims data from January 2002 to December 2020. We included patients diagnosed with CHD under one year of age. GR was defined as an idiopathic growth hormone deficiency or short stature on the claims data. We investigated the neonatal risk factors for GR. RESULTS: The number of patients diagnosed with CHD within the first year of birth was 133,739. Of these, 2,921 newborns were diagnosed with GR. The cumulative incidence of GR was 4.8% at 19 years of age for individuals diagnosed with CHD at infancy. In the multivariable analysis, the significant risk factors for GR were preterm birth, small for gestational age, low birth weight, respiratory distress, bronchopulmonary dysplasia, bacterial sepsis, necrotizing enterocolitis, feeding problems and cardiac procedure. CONCLUSION: Several neonatal conditions were significant risk factors for GR in CHD patients, and appropriate monitoring and treatment programs are required in CHD neonates with these factors. Considering this study is limited to claims data, further studies are warranted, including genetic and environmental factors affecting GR in CHD patients.