The emergence of resistance in microorganisms on a global scale has made it necessary to search for new antimicrobial factors. Antimicrobial peptides (AMPs) seem to meet these expectations. AMPs are produced by bacteria, viruses, plants, and animals, and may be considered as a new class of drugs intended for the prophylaxis and treatment of both systemic and topical infections. The aim of this study is to review the results of studies on the use of peptides to combat infections in vivo. Antimicrobial peptides may be applied topically and systemically. Among the peptides used topically, a very important area for their application is ophthalmology. AMPs in ophthalmology may be used mainly for the protection of contact lenses from ocular pathogens. Many AMPs are in clinical trials for application in the therapy of local infections. There may be mentioned such preparations as: pexiganan (magainin analogue), MX-226 (based on indolicidin), NEUPREX (isolated from human BPI (bactericidal/permeability-increasing) protein), IB-367 (variant of porcine protegrin), P113 (based on histatin), daptomycin, polymyxins, as well as peptidomimetics. In the combat against systemic infections are used such peptides as: P113D (modified P113 peptide containing D-amino acids), colistin, peptoids, and peptides containing non-typical amino acids or non-peptide elements. AMPs are also used as antiprotozoal, antifungal, antitoxic and immunostimulatory agents. The limitations in the use of peptides in the treatment of infections, such as susceptibility to proteolysis, and resistance of microorganisms to the peptides, are also discussed. AMPs are a promising strategy in the fight against microbial infections.