Neonatal hydrometrocolpos is a rare condition that follows congenital vaginal obstruction. Association with urinary obstruction and upper tract dilatation has been reported in some cases. Obstruction of the gastrointestinal tract without a coexisting bowel anomaly can also occur, but this is very rare. In some cases, preoperative diagnosis may be difficult. We describe our experience with a rare case of huge hydrometrocolpos presenting as neonatal intestinal and urinary obstruction.