Background: Müllerian duct anomalies are congenital malformations of the female genital tract and may be of various types. For decades they have been classified according to the American Society of Reproductive Medicine, which mentions unicornuate uterine malformations as the second subgroup. They result from the arrested development of one of the Müllerian ducts and appear in approximately 1/1000 women. These anomalies are usually diagnosed in the second decade of life, because they tend to remain asymptomatic until adolescence and their initial symptoms may vary. Patients present with symptoms such as dysmenorrhea, infertility, and chronic or acute abdominal pain. Case presentation: We report on a 21-year-old Caucasian German patient who suffered from dysmenorrhea for 7 years. After a transvaginal ultrasound and magnetic resonance tomography of the pelvis was performed, the patient underwent a diagnostic hysteroscopy and operative laparoscopy, and was finally diagnosed with a Müllerian duct anomaly presenting with a non-communicating rudimentary uterine horn. The left tube arose directly in orthotopic location from the cornua of uterus, with no connection to the rudimentary uterine horn or structure. Conclusion: The anatomic features of this case have not been reported previously and were not consistent with any existing classification. More cases are needed in order to confirm our hypothesis. Gynecologists should always consider Müllerian anomalies as an important differential diagnosis in young patients with abdominal pain.