Objectives Fraser syndrome is a rare congenital malformation characterized by cryptophthalmos, syndactyly and urogenital tract malformations. The association with hydrometrocolpos is infrequent, with only a few cases reported in the literature. Case presentation A 19-year-old primigravida presenting at 35 weeks of gestation, with prenatal finding of hydrometrocolpos associated with hypotelorism and microphthalmia. Pre-term cesarean delivery was performed due to breech labor and perinatal death. The autopsy confirmed hydrometrocolpos secondary to vaginal atresia and imperforate hymen, associated with cryptophthalmos, syndactyly, nasal and pinna malformations, confirming the diagnosis of Fraser syndrome. Conclusions Fraser syndrome is usually a postnatal diagnosis. The association with genital abnormalities explains the finding of hydrometrocolpos, which could be considered a diagnostic criterion for this syndrome.