A 7-week-old infant was presented at the emergency department with an abdominal mass, unilateral swelling of the groin and suspicion of an inferior caval vein syndrome with bluish discolouration and oedema of the lower extremities. Abdominal imaging showed two large cysts and profound bilateral hydronephrosis. Following laparotomy, an extreme hydrocolpos and an overdistended urinary bladder were found. These findings turned out to be secondary to a transverse vaginal septum. She was treated surgically and was hospitalised for 2 weeks. Long-term follow-up showed normalisation of previously present hypercalciuria and hydronephrosis. A hydro(metro)colpos should be considered in the differential diagnosis of a female infant presenting with an abdominal mass, to apply the appropriate investigations and therapy.