A panel of monoclonal antibodies (MAbs) raised against an Indian strain of Japanese encephalitis (JE) virus was used to map topographically the epitopes on the envelope protein. Two separate clusters of epitopes were revealed. On the basis of reactivity in haemagglutination inhibition (HI), neutralization (NT), passive protection and antibody-dependent plaque enhancement (ADPE) assays with the MAbs, five functional domains (A, B, C, D and E) were delineated. The flavivirus cross-reactive domain for HI (A) was distinct. The JE virus-specific domain for HI (B) was in continuum with those domains representing non-HI JE virus-specific MAbs (C) and flavivirus cross-reactive MAbs (D). Domain E, which mapped close to domain D was represented by two MAbs that reacted with both JE virus and uninfected cell nuclei. Four conclusions can be drawn. (i) Two distinct antigenic domains were associated with HI, (ii) HI and NT in vivo and in vitro were dissociated functions, (iii) ADPE activity was solely linked with the A domain and (iv) all MAbs reacting with epitopes in the B domain had HI/NT/protective activity but failed to show ADPE. The B domain might therefore be considered the most suitable for development of synthetic or genetically engineered vaccines.