Congenital absence of the uterine cervix and vagina in the presence of a functional endometrium is an extremely rare congenital anomaly. Women born with this anomaly present with collection of blood in the uterine cavity or hematometra, disabling pelvic pain and progressively worsening endometriosis. Presented is a case of a 16 year-old girl with severe pelvic endometriosis and hematometra complicated by cervicovaginal agenesis. She was managed by total abdominal hysterectomy with bilateral salpingectomy, left oophorocystectomyandadhesiolysis. Surgical management of congenital cervicovaginal agenesis remains controversial. The decision to do a conservative surgical procedure or a hysterectomy depends on the clinical profile of the patient, the expertise of the surgeon, the extent of the malformation and its association with other mullerian anomalies.