Agenesis of the internal carotid artery (ICA) is a rare congenital anomaly occurring in less than 0.01% of the population, often incidentally discovered in pediatric populations. We recognized a high incidence of additional congenital malformations in children with ICA agenesis. Our study reports nine cases of ICA agenesis and co-existent malformations and discusses implications of the association. We conducted a retrospective chart review of nine children evaluated at our institution with imaging findings of ICA agenesis. Seven children (78%) had congenital aortic or cardiac anomalies including coarctation (4), hypoplastic left heart (1), tetralogy of Fallot (1), and muscular ventricular septal defect (VSD) (1). Four children were diagnosed with an inherited disorder: Alagille syndrome (1), PHACE syndrome (1), VACTERL association (1), and methylenetetrahydrofolate reductase (MTHFR) gene variant (1). Additional congenital anomalies are also described. In the setting of ICA agenesis, we report a robust association with congenital aortic and cardiac anomalies, as well as a broad spectrum of additional anatomical abnormalities that can occur in the setting of known genetic syndromes or as isolated findings. Knowledge of the natural history of ICA agenesis and associated anomalies will guide optimal care for these children.