Unilateral cyst of the seminal vesicle, ipsilateral ectopic ureter, and ipsilateral renal aplasia are the components of a rare congenital abnormality affecting the male urogenital tract. The clinical picture is characterized by a retrovesical cystic tumor, which may cause nonspecific symptoms. Differential diagnosis includes cysts of the müllerian duct, the urogenital sinus/ejaculatory duct, and the prostate. We report a case of a left seminal vesicle cyst associated with aplasia of the left kidney in a 14-year-old boy. Preoperatively, an ipsilateral renal agenesis was suspected, but a renal aplasia with an ectopic urinary megaureter into the seminal vesicle was found intraoperatively. An 8-cm cystic left seminal vesicle and an ipsilateral renal aplasia was successfully removed by operative laparoscopy. The advantages of the laparoscopic approach over open surgery include excellent exposure of the deep pelvic structures, a short hospitalization, and a rapid recovery for the patient. We searched the literature to review the clinical presentation, diagnostic procedures, differential diagnosis, and therapeutic treatment options for this anomaly.