I have been diagnostic with perianal abscess, currently taking flagyl. i don't have swelling , will the abscess affect my reproductive glands (male), ?

Has it been drained?: Most abscesses - perinatal is no exception - requires an incision and drainage. Once source control is achieved, then it should not pose any danger to your reproductive organs. Antibiotics alone will not cure you of this type of infection.

No effect: Most perianal absceses are from pilonidal cyts. If the antibiotics such as Cipro (ciprofloxacin) and Flagyl don't bring the infection under control then excision or drainage is indicated. These infections do not produce orchitis where impairment of testicular function could happen.