Obstructive vaginal and uterine anomalies including imperforate hymen, transverse vaginal septum, and vaginal and/or cervical atresia or aplasia, might rarely present in infancy or childhood with hydrocolpos and/or hydrometra but they usually go unrecognized until presentation with amenorrhea and hematocolpos and/or hematometra in puberty. They should always be included in the differential diagnosis of a suprapubic and/or introital mass; in the latter case, vaginal vascular malformations and vaginal tumors should also be considered. Uterovaginal aplasia typically manifests with amenorrhea in puberty and needs to be differentiated from complete androgen insensitivity syndrome and gonadal dysgenesis of genetic males. Uterine fusion anomalies usually present with fertility and/or obstetrical complications in adulthood. However, a unicornuate uterus with a blind rudimentary contralateral horn containing functioning endometrium, and didelphys or septate uterus with a deviating obstructive septum might present in childhood or puberty with sequelae related with secretions or menstrual retention. This review provides a collective account of the most clinically important information about vaginal and uterine anomalies in childhood and adolescence for clinicians involved in the care of young females with the aim to provide guidance in appropriate evaluation and management.