A case of vesical endometriosis with unilateral renal agenesis is reported. A 13-year-old girl complained of difficulty in urination and lower abdominal pain during the menstruation. Detail urological examinations revealed left renal agenesis and intravesical cystic mass. The mass was located in the left vesical lateral wall, obstructing the vesical outlet and containing dark-brown-coloured fluid in it. She finally suffered from urinary retention following the menstruation and underwent a resection of the mass together with a part of the vesical wall. During the operation, the uterus was found to be a bicornate one. The resected mass was diagnosed as an endometriosis based on the histological findings. Eighteen months after the operation she is free from any symptoms during the menstruation and recurrence of endometriosis.