Reprotonation of polyaniline base with various acids opens a way to conducting materials widely differing in physical properties. The thermal stability of the resulting polyaniline salts was tested by measurements of the conductivity at 125 °C for up to 500 h. Polyaniline sulfate was the most stable and its resistivity increased only by 3.6 times after that time. The stability differed considerably depending on the acid used for reprotonation. The room-temperature conductivity of polyaniline salt is determined by the strength of the acid and its ionic bond with the imine nitrogen in polyaniline. The thermal stability of conductivity, however, is controlled by the ability of the acid to constitute hydrogen bonds with the secondary amine nitrogens in polyaniline. For that reason, oxygen-containing counter-ions, such as sulfates or sulfonates, produce more stable salts with polyaniline, compared with polyaniline protonated with, e.g., hydrochloric acid. The presence of hydroxyl group in the counter-ions also enhances the thermal stability of the polyaniline salt. These conclusions are supported by the analysis of FTIR spectra.