Chylous ascites is a rare entity in infants. An uncommon cause of chylous ascites is intestinal malrotation. We report a case of a neonate with heterotaxia-polysplenia syndrome and intestinal malrotation who presented with chylous ascites and subsequently developed duodenal obstruction from midgut volvulus. He was successfully treated with peritoneal drainage, surgical intervention, and nutritional support. A brief overview of the association of chylous ascites, intestinal rotational anomalies and heterotaxia syndromes is discussed.