Nowadays, a number of antibiotic-resistant bacteria strains is increasing. It is a serious clinical problem and poses a threat to the effectiveness of conventional antibiotic therapy. Thus, scientists are constantly seeking new alternatives for treatment of infectious diseases. There are some natural endogenous factors, which possess antimicrobial activities against a large number of microorganisms, including both Gram-positive and Gram-negative bacteria, viruses and fungi. These factors are present in all eukaryotic organisms and constitute an essential element of their immune system. A large number of in vitro and in vivo models have been used to show the activity of antimicrobial factors, and only few studies have been conducted on people. Results indicate that administration of these molecules is therapeutically beneficial. This review summarizes knowledge of selected endogenous antimicrobial agents, such as cathelicidins, defensins, histatins, lysozyme and lactoferrin. We also discuss potential uses of these factors in the treatment of infectious diseases.