A case of seminal vesicle cyst associated with ipsilateral renal agenesis was experienced recently in our clinic. A 23-year-old male presented with a complaint of right hemiscrotal pain. Right kidney was not visualized by excretory urography. Cystoscopic examination revealed the absence of the right half of trigone and the right posterolateral wall bulging into the bladder, suggestive of an extrinsic mass displacing the bladder wall. Ultrasonography and computerized tomographic scan showed a large cystic mass in the right side of the retrovesical region. Exploratory operation disclosed that the cystic mass was part of the dilated seminal vesicle. Seminal vesiculectomy was done. Many cases of seminal vesicle cyst are associated with a simple or complex malformation of ipsilateral upper urinary tract (renal agenesis, dysplasia, hypoplasia and ectopic ureter). We speculate that most of the benign seminal vesicle cysts are formed as a congenital anomaly due to defective mesonephric duct development which causes concomitant malformations in the upper urinary tract.