Abstract Bardet-Biedl syndrome is an autosomal recessive disorder. It is characterized by cardinal anomalies including retinal dystrophy, digital malformations, mental retardation, obesity, and hypogonadism. Recently, renal anomalies also are mentioned among the cardinal signs. Although association of genital anomalies among affected boys are well known, the association of vaginal atresia and other structural genital anomalies are not mentioned among the less-common manifestations of Bardet-Biedl syndrome in girls. Two girls with Bardet-Biedl syndrome presented with hematometrocolpos in the preadolescent period and vaginal atresia was diagnosed. After surgical treatment and extended hospitalization, uncontrolled sepsis resulted in progressive renal failure and death of both patients. Vaginal atresia is often delayed or missed in the early childhood period. In girls with Bardet-Biedl syndrome, vaginal atresia or other structural genital anomalies should be evaluated more systematically during the initial diagnosis of the syndrome. In infancy, the evaluation of a child with vaginal atresia also should include the differential diagnosis of Bardet-Biedl syndrome. Vaginal atresia may either form a component of the syndrome, or girls who present with vaginal atresia in addition to other components of Bardet-Biedl syndrome might form a distinct entity.