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INTRODUCTION Zinner's Syndrome is a triad of mesonephric duct anomalies comprising unilateral renal agenesis, seminal vesicle cyst, and ejaculatory duct obstruction. In this study, we present a kidney recipient with ectopic ureter associated with Zinner's syndrome and a literature review. CASE PRESENTATION A 59-year-old male with a history of chronic kidney disease and left renal agenesis underwent deceased donor kidney transplantation. After securing optimal renal functions, the patient underwent abdominal computed tomography (CT) scan for the seroma that occurred under the incision. The final diagnosis was an ectopic distal ureter ending in the seminal vesicle cyst's wall and ipsilateral renal agenesis. The patient was discharged without any complications and the clinical follow up was uneventful. DISCUSSION AND CONCLUSION Congenital seminal vesicle disorders are usually associated with ipsilateral urinary duct anomalies stemming from the same embryonic structure. To our knowledge, this is the first case report that describes kidney transplantation in a patient with ipsilateral renal agenesis and ectopic ureter ending in the seminal vesicle cyst. In patients with renal agenesis, during the ipsilateral urinary tract anastomosis, the possibility of ectopic ureter should be kept in mind otherwise graft loss can occur with a high morbidity rate.