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Background: Measles virus has been classified into 22 genotypes. The present report examines the molecular epidemiology of measles virus in Japan from 1984 to 2002, and the epidemiological link between imported cases in several foreign countries and Japanese strains was elucidated from the literature. Methods: B95a or Vero cells was used to isolate the measles virus. The measles virus genome was amplified in the N and H genes by reverse transcriptase-polymerase chain reaction and were partially sequenced. Phylogenetic analysis of a partial sequence of the N gene, from position 1230 to 1685, of the recent measles strains was performed in comparison with the World Health Organization reference strains. Results: There were large outbreaks of measles in Japan in 1984, 1987−1988, 1991−1993, and 2001−2002 and each outbreak was caused by a different genotype. Genotype C1 was an indigenous strain for a long period before 1985, while D3 was isolated in 1987−1988 and D5 in 1991−1993 outbreaks. In addition, the Chicago-type D3 caused sporadic regional outbreaks from 1998 to 1999. After 2000, H1 became the dominant circulating strain. It should be noted that the Japanese strains were detected as imported cases by epidemiological linkage in several countries. Conclusion: Among the recent circulating strain of measles virus in Japan the genotype H1 was dominant after 2000 and the Japanese strains D3, D5, and H1 were exported to several countries. It is recommended that Japan should adopt a more extensive and active vaccination strategy for measles elimination in line with other countries in the world. [ABSTRACT FROM AUTHOR]