Certain ejaculate infections can be traced back to sexually transmitted microorganisms, such as Neisseria gonorrhoeae, Chlamydia trachomatis, Ureaplasma urealyticum and Trichomonas vaginalis. To varying extents, these microorganisms cause such classical genital infections as urethritis, epididymitis and prostatitis as well as subclinical genital tract infections. Several different pathomechanisms are under discussion for infection of the ejaculate: reduction of spermatogenesis resulting from testicular damage, autoimmune processes induced by inflammation, direct influence on the spermatozoal function, disturbances in spermatozoal transport, secretory dysfunction of the male accessory sex glands and leukocytospermia with secondary influence on ejaculate parameters. The relevance of these microorganisms for the localization of the inflammatory process within the genital tract are discussed in detail. Their importance for male fertility is a matter of debate. In particular, the significance of C. trachomatis and U. urealyticum, both of which are detectable in the urethra, is still uncertain and cannot be assessed conclusively. Further information allowing delimitation of an infection resulting from bacterial colonization may be provided, on the one hand, by biochemical markers for an inflammatory reaction and indicators of an immune response in the ejaculate, e.g. PMN elastase, complement C3, or coeruloplasmin, and on the other hand, by secretion markers such as alpha-glucosidase, PSA and phosphatase. Whether the assessment of these markers and indicators can help to clarify the inflammatory origin of infertility in individual cases remains doubtful.