BACKGROUND: The age group of Rubella virus (RV) infection in most industrialized nations located in temperate climates, has in large part shifted from children to young adults since introducing of the RV vaccine in late 1960's. Interestingly, there were rubella outbreaks from 1995 through 1996 in Korea, and middle and high school students were mostly affected during that time. Although continued cycling of the rubella epidemics, there were no reports about the isolation or genetic information of rubella viruses circulated in Korea. METHOD: To isolate RV circulated in Korea, and determine the phylogenetic relationship between RV strains in Korea and RV isolates from other geographic regions including vaccine strains, we inoculated nasopharyngeal secretion samples from clinically diagnosed rubella patients to Vero E6 cells, and sequenced corresponding region of the 5' E1 encoding genomic regions of RV isolates. RESULT: Seven RV strains isolated from Korea showed 93.6 to 97.8% and 98.3 to 100% sequence homologies in nucleotide and amino acid levels, respectively, compared to RA27/3 vaccine strain. Phylogenetic tree based on 359bp of RV indicated that at least two different groups of RV circulated in Korea during 1995-1996 epidemics. CONCLUSION: Our data suggested that mutant RV strains were possibly not the cause of recent rubella epidemics in Korea.