Together with hepatitis C virus and Pestivirus genera, flaviviruses belong to the Flaviviridae family of positive singlestranded RNA viruses. The genus Flavivirus consists of a number of medically important viruses such as yellow fever, West Nile (WN), Japanese encephalitis (JE), Murray Valley encephalitis (MVE), and dengue (DEN) viruses (25). While yellow and dengue fevers may deteriorate into life-threatening conditions, an acute, apparent infection with encephalitogenic flaviviruses rapidly progresses to lethal flavivirus-induced encephalitis in almost one-quarter of infected patients (21). The recent emergence of the flavivirus WN virus in New York State and its rapid spread to surrounding states in North America is an alarming event (29), in addition to the long-standing risk imposed by JE and DEN viruses in other parts of world. There are almost 20 serologically unrelated flaviviruses implicated in human diseases for which there is no vaccine or antiviral treatment available. The majority of these viruses are arthropod borne with an amplifying vertebrate host serving as a natural reservoir and a mosquito or tick vector needed for further dissemination of the virus in nature. Although humans often represent an accidental dead-end host for the virus (21), the incidence of flavivirus-mediated diseases in human populations may expand to either seasonal outbreaks or even localized epidemics causing a major concern to public health. In the absence of an adequate vaccination program, the host natural resistance to flaviviruses as well as development of appropriate antiviral therapies gain importance as alternative approaches for the prevention of diseases caused by flaviviruses (3, 44).Involvement of genetic factors in the resistance to flavivirus infection is difficult to estimate in humans. In contrast, mice carry a genetic trait conferring resistance to flaviviruses that is widely distributed among wild mice populations and rare among laboratory mouse strains (34). Only a few strains of laboratory mice have preserved this trait; among these are PRI, CAST/Ei, CASA/Rk, and MOLD/Rk (34). Some of these strains have been used for backcross breeding to flavivirussusceptible C3H/He mice, resulting in the development of new congenic flavivirus-resistant mouse strains: C3H.PRI-Flv r mice, which carry the resistance allele from outbred PRI mice (12); C3H.M. domesticus-Flv r -like mice, which are derived from flavivirus-resistant wild Mus musculus domesticus; and C3H.MOLDFlv mr mice, which carry the resistance allele from MOLD/Rk mice (38,45).Flavivirus resistance in mice is controlled by a single locus, flavivirus resistance (Flv), on mouse chromosome 5 (31, 44). Although we have defined a narrow region on mouse chromosome 5 that carries the Flv locus by low-and high-resolution genetic and physical mapping, those studies have not clearly identified the critical boundaries of the Flv segment within a larger genomic region of ϳ31 centimorgans that is polymorphic between susceptible C3H/He and resistant C3H.PRI-Flv r mice ...