Benign Cystic Mesothelioma (BCM) is an uncommon peritoneal lesion that usually occurs in reproductive age females with a history of abdominal surgery. Occasional expression of estrogen and progesterone receptor in these cells may explain female predilection. Reports of BCM in males are rare. We describe a case of BCM associated with ipsilateral renal agenesis in a young male without any surgical history. The cyst lining stained positive for cytokeratin, Wilms Tumor-1, epithelial membrane antigen, CD10, estrogen receptor, and progesterone receptor, and negative for PAX-8. Only three cases of BCM associated with congenital renal anomalies have been reported. To the best of our knowledge, this is the first case of BCM associated with ipsilateral renal agenesis in an adult male and the first male case of BCM displaying estrogen and progesterone receptor positivity. Such a case reveals the presence of congenital anomalies should be considered in patients with BCM.