Seminal vesicle cysts with ipsilateral renal agenesis is rare. When the patient is symptomatic, surgical treatment may be necessary. However, the seminal vesicle is difficult to access surgically, and current transurethral or open surgical approaches have inherent shortcomings. The laparoscopic techniques developed in the last decade may overcome the difficulties in the surgical treatment of seminal vesicle pathology. In this study we report a patient diagnosed with left seminal vesicle cyst and ipsilateral renal agenesis who was managed successfully through the laparoscopic approach. The patient was a 41-year-old who suffered from perineal pain and intermittent hemospermia for 20 years. Ultrasonography and computerized tomography, CT, indicated a cyst of the left seminal vesicle and an absent left kidney. The total laparoscopic operation time was 90 minutes and the estimated blood loss was 80 ml. With a follow-up of 13 months, the patient had total relief of his preoperative symptoms without complication.