Twenty-six strains of rubella virus were compared with each other for a molecular epidemiologic study of the virus in three East Asian countries, using the E1 gene of 1443 nucleotides and the following 41 nucleotides in a noncoding region. Nucleotide substitution rates among strains were 0.0–9.4/100 nucleotides. A phylogenetic tree drawn indicated that 2 of 3 Chinese strains were quite different from the other 24 strains; all isolates in the 1960s were classified into a single group independent of the place of isolation, which includes isolates from Japan, the United States, and the United Kingdom; 11 strains of Japanese isolates collected during 1976–1991 made one subbranch derived from the 1960s group; and 2 isolates from the northeast part of Japan in 1990 made a third but minor unique branch. Therefore, at least two groups of the virus cocirculated in Japan around 1990. Antigenic variation of the virus was very small among these strains.