A total of 1,335 archived human sera collected in 1985 from an area in Japan where a tick-borne disease is endemic were examined by indirect immunofluorescence antibody test (IFAT) to estimate seroprevalence against three serologically distinct types of Babesia microti-like parasites; namely, Hobetsu, Kobe, and U.S. types. Eighteen sera (1.3%) were found to be IFAT-positive (titer 1:100-1:6,400), of which 14 and three were ascertained by Western blot analysis to be positive against the Hobetsu and Kobe types, respectively. In addition, four sera showed an IFAT titer of 1:100 against the U.S. type, but they appeared to be false-positive because they were cross-reactive against the Hobetsu and Kobe types, and also because a U.S.-type parasite has not been found in Japan. Our results suggest that human babesiosis in Japan occurred prior to the discovery of the index case in 1999 and that the infections were caused mainly by Hobetsu-type parasites.