The concurrent occurrence of colonic atresia, malrotation, and Hirschsprung’s disease in neonates is extremely rare. These anomalies often share embryologic origins and present overlapping clinical symptoms that complicate diagnosis and management. We report two neonatal cases with this rare triad. Case 1 involved a term neonate initially diagnosed with esophageal atresia and later found to have colonic atresia, malrotation, and Hirschsprung’s disease. Case 2 was a preterm neonate presenting with abdominal distension and perforation, ultimately diagnosed with the same triad. Both underwent staged surgical management, including Duhamel’s procedures after confirming aganglionosis. Awareness of the possible coexistence of these anomalies is essential in neonates with colonic atresia and non-fixed colon. Surgical planning should anticipate aganglionosis and include rectal biopsy. This report emphasizes the importance of early suspicion and multidisciplinary approach for optimal outcomes.