Comparative sequence analysis of a 354 nt fragment of the NS5 region of hepatitis G virus (HGV) isolates was performed to assess two levels of HGV genomic variability: (1) heterogeneity of HGV within an infected individual, and (2) heterogeneity of different HGV isolates. Comparison of nucleotide sequences of DNA clones from two virus isolates demonstrated that in each infected individual HGV is represented by a population of virions with closely related but heterogeneous genomes (quasi-species). Phylogenetic analysis of nucleotide sequences of 42 isolates collected from 14 countries revealed less significant genome variability of HGV as compared to hepatitis C virus. Sequences of all HGV isolates fell into one group of distribution of evolutionary distances. On a phylogenetic tree all HGV sequences segregated into numerous branches. All sequences of isolates from Africa, South and South-East Asia, however, were clustered together and were separated from those of other isolates collected in Europe, North America and Central Asia.