Federation b Russian State Agrarian University -MAA named after K.A. Timiriazev, Moscow, Russian FederationAbstract A comparative analysis of distributional density of the DNA regions potentially predisposed to quadruplex formation was conducted on proviral DNA encoding hemagglutenin (HA) and neuroaminidase (NA) of the avian influenza virus, and also on the env and pol genes of bovine leukemia virus. We discovered that increased genetic heterogeneity of the HA gene coincides with the high frequency of appearance of nucleotide sequences predisposed to G4 quadruplex formation compared to the NA gene. Similar tendency was observed during the comparison of distribution of potential G4 quadruplexes in the env and pol genes of the bovine leukemia virus. Data obtained allowed to suppose that non-overlapping sequences with relatively heightened predisposition to G-quadruplex formation can reflect, to a large extend, recombination events. And variable sequences can reflect the nucleotide context that contributes to appearance of new mutations. In the present article we discuss possible connection between increased density of non-canonical nucleotide structures in genes, products of which interact with receptors of target cells, and their genetic heterogeneity supported in the host-pathogen system.