A baby girl with prenatal diagnosis of complex cardiac anomalies and diaphragmatic hernia was born at 36 weeks of gestation. At 4 hr of life, the baby developed respiratory distress and was intubated. She was found to have right hetetrotaxy with total anomalous pulmonary venous drainage into the portal vein, five hepatic veins draining the liver and intrathoracic herniation of the stomach. The child also developed abdominal distension on the second day of life with passage of scanty meconium. The diagnosis of Hirschsprung's disease (HD) was confirmed by histology. HD in association with right heterotaxy has not been reported earlier. The association of heterotaxy with HD in our patient raises a possible genetic link between the two anomalies that needs further research.