We report a female newborn baby who presented with vomiting and abdominal distension on day 21 of life. Examination revealed facial puffiness, open posterior fontanelles, dry skin, cold peripheries and prominent abdominal veins with visible peristalsis. Barium enema revealed dilated proximal colon, empty rectum, funnel like transition zone between proximal dilated and distal constricted bowel. Serum TSH level was >;150 uIU/mL. Biopsy revealed aganglionic segment suggesting Hirschsprungs disease, an unusual association with congenital hypothyroidism.