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The cause of epididymitis is usually a bacterial infection. The bacteria usually get to the epididymis by moving back through (retrograde) the urethra, prostate, vas deferens into the epididymis. The responsible bacteria are usually identified in about 80% of cases.

Two main groups of organisms cause most cases of epididymitis: sexually transmitted organisms and coliforms (organisms that commonly live in the intestines).

In men younger than about 39 years of age, the causes are usually the same organisms that cause the sexually transmitted diseases of chlamydia (responsible for nearly 50%-60% of cases) and gonorrhea. The bacterial species are Chlamydia trachomatis and Neisseria gonorrhea, respectively.

In those older than 39 years of age, the causes are usually coliforms, which are bacteria (such as Escherichia coli) that live in the intestines. These organisms also frequently cause bladder infections. Any age of men who participate in anal intercourse are more likely to get infected with E. coli or other fecal bacteria. Epididymitis is rarely caused by fungi or Mycobacterium spp.

Chemical epididymitis (rare) is inflammation caused by the retrograde (backward) flow of urine when exercising or having sex with a full bladder.

Amiodarone (Nexterone), a frequently used heart medication, occasionally causes inflammation of the epididymis.

Viral infections (including mumps), mainly in the pediatric population.