ABSTRACT. The first case of human babesiosis was reported in Japan. The epidemiology of this disease in Japanese nature remains unclear. In this study, 97 common field mice captured in Hokkaido, Japan, were examined. Blood specimens absorbed onto filter papers were eluted and tested by nested PCR using specific primers for the B. microti nuclear small subunit rRNA genome. Twenty-three percent (11/47) of Apodemus speciosus and four percent (2/50) of Clethrionomys rufocanus were positive. The 159-bp primary sequences of PCR products tested exhibited 97.5% and 96.8% homology with those of the human isolate in Japan and of U.S. strains of B. microti, respectively. KEY WORDS: Babesia microti, filter paper, rodent.