This case was an extremely rare form of cervical dysgenesis that presented with cyclic pain. Diagnostic laparoscopy and vaginoscopy showed the presence of a blind uterus at the level of the internal cervical os with a normal vagina and exocervix. Mullerian ducts are the embryologic origin for the uterus, cervix and upper part of the vagina. Mullerian duct migration initiates from the upper part of the Mullerian system. Therefore an obstructed uterus is usually associated with cervical and upper vaginal anomalies. This case was unusual because of the presence of an isolated segmental atresia at the level of the internal cervical os. However the vaginal portion of the cervix, vagina and urinary system were normal. We theorized that the absence of an appropriate fusion between the Mullerian duct and its underlying mesoderm, loss of cell-to-cell communication and special gene expression during a critical time period or a vascular accident between 12–22 weeks of gestation might have caused this anomaly. The patient underwent a laparotomy to create a utero-cervical canal using a peritoneal graft.