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Murine typhus (etiologic agent: Rickettsia typhi) is endemic to Indonesia, especially on the highly populated island of Java. A survey of rodents from Irian Jaya, the eastern-most province of Indonesia, indicated striking geographic variation in risk factors associated with murine typhus. Murid rodents (n = 112) collected from two villages in the Arso district of northeastern Irian Jaya, were found to be free of ectoparasites normally associated with transmission of R. typhi (i.e., Xenopsylla cheopis). All rodents (n = 72) tested by enzyme-linked immunosorbent assay were negative for antibodies to R. typhi, whereas 12.5% (9/72) were positive for antibodies to Orienta tsutsugamushi. In contrast, both Rattus norvegicus and R. rattles (combined n = 87) from the harbor area of the provincial capital, Jayapura, were infested with flea ectoparasites. X. cheopis was found on 31 (35.6%) of the live-captured rodents. Serum samples from nine of 82 rodents contained antibodies reactive to R. typhi (11.0%). These data show for the first time that rodents exposed to R. typhi are well established in Jayapura, and that some of these rodents harbor fleas potentially capable of transmitting murine typhus and plague.