Male urogenital tract infection (UTI) is one of the most important causes of male infertility, being associated with 8%-35% of male infertility. Pathogenic bacteria may interfere with infertility treatment involving the application of in vitro fertilization. Microorganisms might affect the spermatozoa function in different ways: (a) By direct contact on sperm cells; by the help of some organelles such as pili; causing agglutination of motile sperm, reducing ability of the acrosome reaction, and also causing alterations in cell morphology. (b) Trigger a local inflammatory reaction leading to increase in reactive oxygen species (ROS). (c) Induction of sperm autoantibodies. (d) Production of cytotoxic factors. (e) Infection treatment with antibiotics for long time may lead to defect in the sperm. The most frequently isolated bacteria from semen samples include Staphylococcus aureus, Escherichia coli, Streptococci, Klebsiella sp, Mycoplasma hominis, Chlamydia trachomatis and Enterococcus faecalis. The infection with these bacteria has significantly negative effect on sperm parameters and DNA integrity. DNA fragmentation may cause infertility, miscarriage, and birth defects in offspring. Therefore it may be a more objective marker of sperm function. The exact molecular mechanism of how bacteria affect chromatin and sperm nuclear protein still unknown. The bacterial infections lead to premature emergence of histone H3 methylation at lysine 79 (trimethylated H3K79) and hyperacetylated H4 which simultaneously occurred with transition protein TNP1. In mammals, reduced levels of histone H4 hyperacetylation correlates with impaired fertility. Further researches on this topic are necessary.