Neonatal hydrometrocolpos (HMC) is a cystic dilatation of a neonate's vagina and uterus occurring secondary to congenital vaginal obstruction, with or without maternal estrogenic stimulation of uterine and cervical glands causing increased secretions during the prenatal and postnatal period. Diagnosis is made using ultrasonography and further confirmed by MRI. HMC in a neonate can rarely present with congenital anomalies such as polydactyly, which may indicate a variety of underlying genetic syndromes. There is a deficit in the literature as to whether the development of HMC in a neonate of consanguineous parents is an isolated finding or solely related to an underlying syndrome. We hope to help bridge this gap by reporting a case of a 12-day-old neonate presenting with hydrometrocolpos and polydactyly, born to consanguineous parents.