An important biological function of hairpin-loop structures is the defense of RNA transcripts from degradation by different factors as well as the transcription regulation due to their formation in transcription terminators. The patterns of thermodynamically stable perfect and imperfect inverted repeats were determined for pXO1 and pXO2 plasmids of pathogenic Bacillus anthracis strains. A sequence analysis of these plasmids has shown the plasmid pXO1 contains 176 inverted repeats, the energy of which varies from –30.6 kcal/mol to –10.0 kcal/mol, and the plasmid pXO2 of B. anthracis contains 57 inverted sequences with energy from –27.2 kcal/mol to –10.0 kcal/mol. Physical maps of the pXO1 and pXO2 plasmids with located hairpins are presented. These hairpin-loop structures are shown to be localized in the sites of regulatory genes or the elements encoding proteins of unknown function.