Zinner syndrome is a rare congenital malformation of the mesonephric duct comprising of seminal vesicle cyst, ipsilateral renal agenesis, and ejaculatory duct obstruction. Clinical presentation varies with perineal pain, painful ejaculation, hematospermia and infertility common presenting complaints. Here, we present a case of Zinner syndrome in a 35-year-old male with a rare clinical presentation of only abdominal discomfort. The purpose of this case report is to highlight the challenging clinical presentation of Zinner syndrome and the use of imaging modalities in diagnosing the condition.