Hirschsprung disease, the colonization defect of neural crest cells through the colon, is one of the reasons for functional obstruction in neonates. Furthermore, hypothyroidism has been known to be one of the causes of bowel hypomotility and pseudoobstruction. These two diseases are generally considered in the differential diagnosis. Although defective thyroid function has been found to be responsible for inappropriate neuronal migration in the brain, the effect of thyroid hormone on neural crest cell migration to the bowel has not yet been evaluated. Here, we report a case with Hirschsprung disease and congenital hypothyroidism, which may point to the need for future studies evaluating the interaction of colonic neural crest cell colonization and thyroid hormone.