To further study the phenomenon of flavivirus persistent infection, golden hamsters (Mesocricetus auratus) were inoculated intraperitoneally with a low pathogenicity strain of St. Louis encephalitis virus (SLEV). After inoculation, the animals remained asymptomatic and developed high levels of specific neutralizing antibodies in their sera. However, about one half of the hamsters continued to shed infectious SLEV in their urine for prolonged periods of time. By co-cultivation, SLEV was recovered from selected tissues (kidney, lung, and brain) of some of the animals for up to 185 days after initial infection. Although no specific histopathologic changes were observed in these tissues, SLEV antigen was shown by immunohistochemistry in the interstitium and tubular epithelium of the renal cortex and in a few large neurons of the cerebral cortex. Seventeen SLEV isolates from urine and tissues of the chronically infected hamsters were sequenced. In comparison with the infecting parent SLEV strain, two common mutations and amino acid substitutions were observed in all of the hamster isolates. The findings of this study were very similar to previous descriptions of chronic West Nile, Modoc, and tick-borne encephalitis virus infections in mammals, and they re-emphasize the potential importance of persistent flavivirus infection in vertebrates.