The Ilheus (ILH) virus has long been known to belong to group B of the arboviruses. Previous attempts to relate it to existing serogroups within the Flavivirus genus using conventional serological techniques such as hemagglutination inhibition, neutralization and complement fixation tests have been inconclusive. We have first used denaturing gel electrophoresis to estimate the molecular weight of immunoprecipitated radiolabeled viral proteins and the cross-reactivity among ILH proteins and hyperimmune sera to several flaviviruses only from the mosquito-borne encephalitis virus serogroups. The estimated molecular weight for the three proteins was in the same order of magnitude, as previously established, for mosquito-borne flaviviruses. Cross-immunoprecipitation tests showed that NS3 protein is the most cross-reactive. Partial nucleotide sequence analyses of the NS3 gene, corresponding to an area linking the helicase and the RNA triphosphatase domains, revealed that ILH virus is very closely related to the Japanese encephalitis virus complex confirming earlier serological data.