The lack of an effective animal model has been a major obstacle in attempts to define the role of humoral and cellular immune responses in protection against flavivirus infection. We have used F-1 hybrid mice (BALB/c x C3H/RV) that are heterozygous for the flavivirus resistance allele Flv(r) and show reduced virus replication in the brain after intracerebral inoculation. F-1 hybrid mice challenged by intracerebral inoculation with Murray Valley encephalitis (MVE) virus developed encephalitis 2-3 days later than a genetically susceptible strain (BALB/c) but showed a similar mortality rate. This delay in the onset of disease provided more opportunity for virus clearance by primed immune responses. Using F-1 hybrid mice we were able to demonstrate protective immunity induced by structural and non-structural proteins of MVE virus by immunization with pure NS1 protein or recombinant vaccinia viruses that expressed various regions of the MVE genome. These constructs included VV-STR (C-prM-E-NS1-NS2A), VV-Delta C (prM-E-NS1-NS2A) and VV-NS1 (NS1-NS2A). VV-Delta C vaccinated mice were completely protected (100% survival) from challenge with 1000 infectious units of MVE virus, while mice inoculated with VV-STR, VV-NS1 or pure NS1 were partially protected (40%, 47% and 85% respectively). Analysis of prechallenge sera and in vivo depletion studies revealed that the solid protection induced by VV-Delta C was mediated by neutralizing antibody to the E protein and did not require a CD8(+) T cell response. The partial protection provided by VV-STR, VV-NS1 and pure NS1 occurred after induction of antibody to NS1. However, depletion of CD8(+) cells prior to virus challenge ablated the protection provided by VV-NS1 indicating some requirement for class I restricted cytotoxic T cells.