Choanal atresia is a relatively common congenital malformation which is often associated with other anomalies. On the other hand, ileal atresia is very rare, mostly nonsyndromic and occasionally associated with other anomalies. The association of choanal and ileal atresia is unknown. Here we report the first instance of bilateral choanal atresia and ileal atresia in a full term male infant and describe the subsequent surgical treatment of both conditions. The association is unique and may represent a syndrome.