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1 Gonorrhea and chlamydia are the most common causes of epididymitis in young, sexually active men. 2  Other infections. 3  For boys and men who aren't sexually active, epididymitis can be caused by a nonsexually transmitted bacterial infection.
In men who are less than 40, most cases of epididymitis are from sexually transmitted diseases. The organisms make their way into the urethra (the tube from which a man urinates and ejaculates) and then work their way backwards into the ejaculatory ducts (the ducts that carry the sperm). The most common organism is chlamydia.