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Introduction Congenital heart defects (CHD) are common and are a frequent subject of research using large administrative databases such as the Pediatric Health Information System (PHIS) database. The capture rate of CHD within PHIS, however, has not been described. Methods The PHIS database includes inpatient encounters from over 52 tertiary care pediatric hospitals across the United States. We identified all patients less than 1 year of age with a cardiac defect in PHIS from 2010 to 2014 and compared these results with national prevalence estimates based on the National Birth Defects Prevention Network annual report, which served as the gold standard. Results The capture rate of CHD in PHIS ranged from 30 to 95% depending on the spectrum of severity and heterogeneity of the cardiac defect. The capture rate was higher for critical CHD (CCHD) at 66%, and all lesions with 70% or greater capture rate (interrupted aortic arch, truncus arteriosus, single ventricle, total anomalous pulmonary venous return, double outlet right ventricle, and hypoplastic left heart syndrome) fell within the CCHD category. Conclusions Just over half of the predicted CHD patients were identified using the PHIS database. Although there is a high capture rate for CHD that require early hospitalization, there is a low capture rate for defects with a wider spectrum of disease presentation. These attributes of the PHIS database should be used to frame previous and future research using PHIS to study CHD.