Hemorrhagic fever with renal syndrome (HFRS) is an infectious disease caused by hantaviruses of the family Bunyaviridae. Among them, Hantaan virus (HTNV) is most widely distributed in Korea. The striped field mouse, Apodemus agrarius, is the natural host of HTNV in rural Korea. We trapped 766 small mammals of three species (1 Eothenomys regulus, 13 Crocidura suaveolens, and 752 Apodemus agrarius) in five provinces in Korea from January to December 2007. We tested 542 rodent sera for HTNV antibodies by an indirect immunofluorescent assay (IFA), finding antibody prevalences of 4 to 29% among the five provinces. Peaks in monthly antibody prevalence occurred in spring and fall. Antibody prevalence during the second peak coincided increased HFRS incidence in autumn. We used multiplex reverse transcription polymerase chain reaction (RT-PCR) to detect the partial S segment of Hantaan, Seoul, and Puumala viruses in 766 lung samples of all captured animals and found HTNV RNA in 25 A. agrarius. Two isolates of HTNV were obtained from PCR-positive A. agrarius by cultivation in Vero E6 cells. This first systemic survey of monthly antibody prevalence in hantavirus hosts in wide regions in Korea could provide useful information for other researchers studying environmental and ecological factors affecting HFRS.