Hydrometrocolpos, occurring in approximately 1/6000 newborn girls, can be caused by a stenotic urogenital sinus, a severe cloacal malformation, but also by other conditions such as an imperforate hymen, a midline vaginal septum and vaginal atresia. The prenatal differential diagnosis of this wide spectrum of conditions is not easy and requires a multidisciplinary approach with follow-up scans and MRI to access the severity of the condition. A non-consanguineous couple was referred in the first pregnancy at 30 weeks. The father, 30 years of age, of Kaukasian origin, and the mother of Asian origin, 26 years of age. Ultrasound at 30 weeks revealed ambiguous genitalia (with suspicion of clitoral hypertrophy), a septated structure located behind the bladder compatible with hydrometrocolpos with a uterine malformation (uterus didelphys), a single umbilical artery, mild ascites and growth on the tenth centile. The differential diagnosis included a vaginal atresia, a urogenital sinus and a more severe cloacal malformation. After serial scans, MRI and counselling by an experienced surgeon the preferential diagnosis of a cloacal malformation was made and a late pregnancy termination was performed. Pathological examination revealed: low vaginal atresia with uterus didelphys, anal atresia with rectovaginal fistula and a normal urinary tractus. The differential diagnosis between hydrometrocolpos due to vaginal atresia or due to a more severe cloacal malformation is not straightforward. Care should be taken in decision making and counselling patients with these complex prenatal malformations.