There is a constant arms race between prokaryotes and their bacteriophage viruses. Thanks to modern methods, in particular, methods of comparative genomics and colocalization search, our understanding of the arsenal of antiphage defense systems in bacteria and archaea has expanded significantly. More than 150 defense systems are already known, and powerful tools such as the online services DefenseFinder and PADLOC, which use HMM profiles, have been developed to search for their genes. The study of the defense systems of pathogenic bacteria and their mechanisms of operation can help in the development of new genetic engineering tools, as well as for medical purposes, in particular, in the use of phage therapy to combat pathogenic bacteria. In this paper, using PADLOC and DefenseFinder, we determined the composition of the defense systems of a number of genomes of intracellular parasites and compared it with the set of defense systems in free-living bacteria.