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Abstract Background The unicornuate uterus is caused by abnormal or failed development of one Müllerian duct. Unicornuate uteri with functioning non-communicating rudimentary horns are susceptible to many gynaecologic and obstetric complications such as hematometra, endometriosis and ectopic pregnancy and thus surgical resection is usually recommended.. Case presentation We report a rare case of a unicornuate right uterus with rudimentary non-communicating (functional) cavitary left horn (class U4a) in a 17-year-old girl who was diagnosed with VACTERL association. She was presented to our centre with 3 years history of secondary sever dysmenorrhea. Pelvic magnetic resonance imaging revealed a normal uterus on the right side, a 7 × 8 cm left endometrioma, a tortuous dilated fluid-filled structure in the left hemipelvis, mostly represented left-sided hematosalpinx, and a well-defined lesion with thick enhancing wall in the left hemipelvis measuring 6.7 × 5.7 × 5.6 cm with a similar enhancement to the uterus in the right. She underwent laparotomy that showed a right unicornuate uterus with a normal cervix and a rudimentary non-communicating distended left horn. In addition, there was a left endometrioma and left hematosalpinx. Resection of the left communicating horn, left salpingectomy and left ovarian cystectomy were performed. The right tube and both ovaries were preserved. At 9-months follow up, the patient had a regular period and the pain subsided completely. Conclusion We report yet the second case of VACTERL association and unicornuate uterus with non-communicating functional rudimentary horn, in hope of expanding the knowledge of a rare occurrence. This case also highlights the importance of considering the diagnosis of Müllerian duct anomalies in patients with a history of other anomalies, and/or history of early-age secondary dysmenorrhea.