BACKGROUND: Among patients with congenital heart disease (CHD), the coexistence of noncardiac congenital anatomic abnormalities (NC), genetic abnormalities (GA), and syndromes (S) may influence therapeutic strategies and outcomes. The appreciated prevalence of these abnormalities has risen because increased screening and improved diagnostic precision enable identification of these comorbidities in a larger fraction of neonates with CHD. We examined the contemporary prevalence and distribution of NC/GA/S across diagnostic groups among neonates undergoing cardiac operations using a large nationally representative clinical registry. METHODS: The Society of Thoracic Surgeons Congenital Heart Surgery Database (STS-CHSD) was queried to identify neonates (=30 days) who underwent index cardiac operations from 2010 to 2013. The fundamental cardiac diagnosis was used to identify 10 diagnostic groups. The prevalence of NC/GA/S was reported across each group. RESULTS: The cohort included 15,376 index neonatal operations from 112 centers. Overall, 18.8% (2,894 of 15,376) of operations were performed in neonates with NC/GA/S. Patients with atrioventricular septal defect (212 of 357 [59.4%]), interrupted aortic arch (248 of 567 [43.7%]), truncus arteriosus (204 of 554 [36.8%]), and tetralogy of Fallot (417 of 1,383 [30.2%]) had the highest prevalence of NC/GA/S abnormalities, whereas those with transposition of the great arteries (111 of 2,778 [4.0%]) had the lowest prevalence. The most commonly identified NC/GA/S included heterotaxy (597 of 15,376 [3.9%]), DiGeorge syndrome or 22q11 deletion (550 of 15,376 [3.6%]), Down syndrome or trisomy 21 (318 of 15, 376 [2.1%]), intestinal malrotation (220 of 15,376 [1.4%]), and Turner syndrome or 45XO (189 of 15,376 [1.2%]). CONCLUSIONS: The prevalence of NC/GA/S varies widely across CHD diagnostic groups. This information may be useful for patient counseling, recommendations for screening for anomalies and genetic disorders, and perioperative management.