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Hantavirus antigens were detected in lung tissues of 8/113 Apodemus flavicollis and 2/17 Clethrionomys glareolus captured in 1984 in Fojnica, a region of Yugoslavia endemic for hemorrhagic fever with renal syndrome; hantavirus antigens were not detected in lung tissues from 126 other mammals collected in Fojnica. Three hantaviruses, 2 from A. flavicollis and 1 from C. glareolus, were isolated directly in Vero E6 cells and were partially characterized. The isolates from A. flavicollis, designated Fojnica virus, were antigenically similar but not identical to Hantaan virus strain 76–118, whereas the isolate from C. glareolus was antigenically indistinguishable from Puumala virus, strain Hällnäs B1. These data are consistent with previous studies that indicate the existence of at least 2 hantavirus serotypes in Yugoslavia.