From the plasma of a 54-year-old woman, who acquired the persistent carrier state of hepatitis B virus through materno-fetal transmission, 49 clones of viral genomes were propagated. They did not reveal any differences in the size and number of cleavage products with any of 11 restriction endonucleases. Randomly selected 5 clones were classified into 3 groups by the variation at 4 positions in the nucleotide sequence of the envelope and core genes. The complete nucleotide sequences were determined for 3 of them, each representing a group, and they all had a genomic length of 3215 nucleotides. Variation was found in from 5 to 11 nucleotides. Assuming the infection with the common ancestor virus at birth, hepatitis B virus genomes in her plasma were estimated to have evolved at a rate from 1.4 to 3.2 x 10(-5) nucleotide substitutions per site per year. This value is 10(4)-fold greater than DNA genomes, 10(2)-fold less than human immunodeficiency virus but in the same order as most RNA viruses including certain retroviruses.