Viruses of the Flaviviridae family are responsible for causing global health epidemics in humans; diseases ranging from encephalitis to hepatocellular carcinoma. Japanese Encephalitis Virus (JEV) is a leading cause of viral encephalitis. The JEV envelope protein (E) facilitates cellular attachment and membrane fusion. The JEV E protein consists of three domains (domains I, II, and III) that are characteristic of all flavivirus envelopes. In solution, the JEV E protein packs as an antiparallel dimer. However, this dimer interface lacks many contacts observed in other flavivirus E structures. Several neutralizing antibodies that recognize the JEV E protein have been identified. Binding-site mapping reveals that these epitopes fall within the domain I lateral ridge, fusion loop, domain III lateral ridge and domain I-II hinge regions. All regions known to be involved in neutralization of the closely related West Nile virus that also causes encephalitis. The JEV E structure implies that mature JEV virions assemble in a more open conformation than observed for related viruses. The variable spacing between E proteins is a possible mechanism for differential recognition by antibodies and cellular receptors.