Introduction: Müllerian anomalies are rare developmental anomalies of the female reproductive tract, that are usually associated with renal abnormalities.Case Presentation: A 16-year-old Sri Lankan schoolgirl, presented with progressive dysmenorrhea and inter-menstrual lower abdominal pain for 2 years. There was recent lower abdominal distention over 6 months. Examination revealed a non-tender mass in the suprapubic area.A subsequent CT scan, followed by an ultrasound abdomen, revealed features of a right-sided unicornuate uterus with a non-communicating left-sided horn containing endometrium and a homogenous large cystic lesion between the non-communicating left horn and the uterine body, associated with ipsilateral renal agenesis.She underwent a laparotomy and resection of the left-side rudimentary horn of the uterus with a left-side ovarian cystectomy, as intra-operative findings suggested an endometrioma.Conclusion: Clinical presentations of Müllerian anomalies are largely non-specific. Early diagnosis and prompt treatment are useful in avoiding complications that arise as a consequence of Müllerian anomalies.