Two different scrapie prion strains with different characteristics were obtained from two sheep naturally infected with scrapie in Japan. In mice transmission, one (Tsukuba-1) showed shorter incubation periods (133+/-2 days) than the other (Tsukuba-2) (288+/-5 days). Spongiform changes and accumulation of an abnormal isoform of prion protein (PrP(Sc)) were observed throughout the brain in Tsukuba-1 inoculated mice, while the lesions and the PrP(Sc) accumulation were localized in the brain stem of mice with Tsukuba-2. Western blot analysis showed that there was no strain-specific glycoform of PrP(Sc) within these two strains. A super-infection experiment revealed that neither strain interfered with the other's propagation.