Abstract West Nile virus (WNV) is a neurotropic arthropod-borne flavivirus that is maintained in an enzootic cycle between mosquitoes and birds, but can also infect and cause febrile syndrome and encephalitis in humans and horses. Diverse pathogenic WNV strains circulate in Africa, the Middle East, Asia, the United States and Europe. Their genetic alignments allowed their classification into two major lineages, lineages 1 and 2. So far, little is known about their virulence and neuropathogenicity. To get insight into the neuropathogenicity of WNV, we compared the neuropathogenic properties of two lineage 1 WNV strains known to have caused many (417) or a few (less than 10) human cases, Israel 1998 (IS-98-ST1) and Kunjin 35911 respectively. Four-week old C57Bl6 mice were inoculated intraperitoneally with both strains and strain virulence was assessed, as well as brain viral load and lesions. Histological examination of brain tissues revealed that the Kunjin 35911 strain is able to induce alterations such as spongiosis, gliosis, meningitis, perivascular infiltrates and neuronal death in nearly all the brain structures studied. On the contrary, spongiosis was not observed in the brains of mice inoculated with the same LD50 of the IS-98-ST1 strain and meningitis, perivascular infiltrates and neuronal death were strongly reduced compared to the Kunjin strain. In addition, our results suggest that the molecular pathways involved in cell damage vary qualitatively and quantitatively between both strains according to the brain structure considered. In conclusion, although the Kunjin 35911 strain is less virulent than the IS-98-ST1 strain, it was found to induce more severe lesions in the brain, demonstrating that WNV genotype influences neuropathogenicity as well as virulence. Based on these results, the comparison of WNV strains might help to elucidate the mechanisms of WNV neurovirulence and neuropathogenicity and to promote the development of novel therapeutic targets.