The imperforate hymen and transverse vaginal septum are female reproductive tract abnormalities. Their concurrent occurrence is rare. So far, no manifestation of both anomalies within the same family has been reported in the literature. We report the first familial case of two sisters having both mentioned abnormalities. Our patient was the youngest sister of a 14-year-old, who presented with cyclic lower abdominal pain. Clinical and imaging examinations showed an imperforate hymen with hematometrocolpos. In addition, the surgery confirmed a low transverse vaginal septum, which was resected using a virginity-preserving procedure. In conclusion, the presence of both mentioned abnormalities between siblings reflects a potential genetic etiology, also in order to avoid late diagnostics of such anomalies, the imperforate hymen must be screened in the birth room.