Strain variation among Japanese encephalitis (JE) virus isolates has been previously demonstrated by many workers using different methods. We report the nucleotide sequence of the 5' non-coding region and the nucleotide and deduced amino acid sequences of structural protein genes for eight wild-type JE virus strain isolated from different Asian countries (Vietnam, Nepal, Indonesia, Thailand, India, Japan and China). We compare these with five other published wild-type JE virus strains isolated from Japan and the mainland of China. No strain variation could be related to geographical location on the basis of the wild-type JE virus strains studied. The viruses differed from each other by between 21 (0.9%) and 111 (4.6%) nucleotides and by between 3 (0.4%) and 31 (4.2%) amino acids over the 2434 nucleotides examined. The amino acid divergence of the envelope (E) protein gene of the viruses was 4.2% or less among the 13 strains compared. Thus there is little genetic divergence in the strains studied. However, four variable E protein amino acids (E-51, E-209, E-244 and E-366) were identified. Residue positions E-51, E-244 and E-366 are found in peptides with functional T helper cell epitopes in two other flaviviruses. Therefore, these amino acids may be important in defining the various immunotypes of JE virus identified by antibody reactivity patterns.