Hydrometrocolpos is a clinical condition that arises from vaginal outflow obstruction during fetal life and rarely manifests with an abdominal cystic mass in the neonatal period. In cases with delayed diagnosis, urinary complications, respiratory distress, and gastrointestinal obstructions may occur and thus a prompt diagnosis is of prime importance for the prevention of such complications via surgical drainage and repair. In the present study, we report on a neonatal hydrometrocolpos case manifesting as an abdominal cyst associated with intrauterine vaginal atresia and causing bilateral hydronephrosis, urosepsis, and respiratory distress.