Two segments of the variable terminal regions of the variola virus (VARV) genome were sequenced in 22 strains from the Russian collection, including about 13.5 kb of the left segment and about 10.5 kb of the right segment. The total length of the sequences was over 540 kb. Phylogenetic analysis of the new and published data determined the relationships among 70 VARV strains, the character of their clustering, and the intergroup and intragroup variation of the strain clusters. Loci with the highest polymorphism rate were identified and proved to map to noncoding regions or to regions of damaged open reading frames, characteristic of the ancestral virus. These loci offer attractive possibilities for developing a strategy of VARV strain genotyping. Recombination analysis by different methods did not detect, except for a single case, significant recombination events in the VARV strains examined.