Two isolates of influenza B virus were obtained in the spring of 1997. One strain, B/Taiwan/ 21706/97, was isolated from a patient who had acute tonsillitis. The other, B/Taiwan/3143/97, was isolated from a patient who was diagnosed with meningoencephalitis. This implies that the influenza B viruses not only cause respiratory symptoms but may also cause inflammation of the nervous system. Sequence analysis of the hemagglutinin (HA) gene, HA1 domain, indicated that there were remarkable amino acid changes in the strain B/Taiwan/3143/97 compared to B/Victoria/2/87, B/Yamagata/16/88, and B/Taiwan/7/88. The changes in the positions 116, 200, 238, 242, and 271 were correlated with receptor binding. Furthermore, a potential glycosylation site at position 233 was lost. In total, 30 amino acid changes were noted at positions ranging from 116 to 295. These changes may affect the antigenicity of the virus. Phylogenetic analyses also showed that the B/Taiwan/3143/97 was located in an independent lineage, when compared to the reference strains belonging to B/Victoria/2/87 and B/Yamagata/16/88 lineages. This supports the hypothesis that influenza B viruses with distinct genetic characteristic were co-circulated in Taiwan.