Between 1983 and 1999, 27 human cases of scrub typhus (two fatal) occurred in the Nodagawa River basin of northern Kyoto, Japan, an area where no cases had been previously reported. Antibody screening of infected patients’ sera showed that nine of 15 patients had high titers against the Gilliam type of Orientia tsutsugamushi (Hayashi). To determine the vector mite transmitting the disease, we studied rodent and chigger populations in and near a rice field alongside the Nodagawa River between 1996 and 1999. The most common rodent species was Microtus montebelli (Milne-Edwards), representing 73.3% (33/45) of the population. The mite index (average number of mites per infested host) was highest (190.8) in Leptotrombidium pallidum Nagayo, Mitamura & Tamiya parasitizing on M. montebelli, followed by Leptotrombidium intermedium (Nagayo, Mitamura & Tamiya) (174.9) on the same host species. Orientia tsutsugamushi was isolated from 60.5% (23/38) of rodents and from 71.2% (37/52) of pools of engorged L. pallidum. The Gilliam type of O. tsutsugamushi was most prevalent in rodents, and in engorged L. pallidum and it was the only type recovered from 10 isolates inoculated into L 929 cells for indirect immunofluorescence examination. Orientia tsutsugamushi infected 14.3% (181/1263) and 14.8% (306/2066) of engorged and unfed L. pallidum larvae, respectively, and was also detected in 0.055% (2/3634) of unfed L. intermedium, although previous studies suggest that this mite rarely bites humans. These results show that L. pallidum is the primary vector species of scrub typhus in this new endemic area in Japan.