We report a case of a 2-year-old boy who presented with an empty left scrotum. Clinical examination revealed a left palpable undescended testis. During orchidopexy, segmental atresia of the vas deferens was found, and microsurgical repair was carried out. Segmental vasal atresia is an extremely rare condition and is infrequently diagnosed, especially in the pediatric age group. This is the first reported case of segmental vasal atresia without an association with cystic fibrosis.