The development of accessible express methods to determine markers of viral diseases in saliva is currently an actual problem. Novel cross-sensitive sensors based on Donnan potential with bio-comparable perfluorosulfonic acid membranes for the determination of salivary viral markers (N-acetyl-L-methionine, L-carnitine, and L-lysine) were proposed. Membranes were formed by casting from dispersions of Nafion or Aquivion in N-methyl-2-pyrollidone or in a mixture of isopropyl alcohol and water. The influence of the polymer equivalent weight and the nature of dispersing liquid on water uptake, ion conductivity, and slope of Donnan potential for the membranes in H+ and Na+ form was investigated. The varying of the sorption and transport properties of perfluorosulfonic acid membranes provided a change in the distribution of the sensor sensitivity to N-acetyl-L-methionine, L-carnitine, and L-lysine ions, which was necessary for multisensory system development. The simultaneous determination of three analytes, and the group analysis of them in artificial saliva solutions, was performed. The errors of N-acetyl-L-methionine and L-carnitine determination were 4-12 and 3-11%, respectively. The determination of L-lysine was complicated by its interaction with Ca2+ ions. The error of the group analysis was no greater than 9%. The reverse character of the viral markers' sorption by the membranes provided long-term sensor operation.