Transmissible spongiform encephalopathies (TSEs), or prion diseases, are fatal infectious neurodegenerative disorders. Their causative agents are prions, which are composed of disease-associated forms of prion protein (PrPSc). Naturally occurring cases of TSEs are found in several mammalian species including humans, sheep, goats, minks, cattle and deer. Prions are also experimentally transmissible to other mammals such as mice, hamsters and monkeys, but interspecies transmission is often inefficient due to the 'species-barrier'. Studies have suggested that the barrier is not only simply determined by differences in amino acid sequences of cellular PrP (PrPC) among animal species, but also by prion strains which are closely associated with conformational properties of PrPSc aggregates. Although the conformational properties of PrPSc remain largely unknown, recent investigation of local structures of PrPC and, in particular, structural modelling of PrPSc aggregates have provided molecular insight into this field. In this review, we discuss the species-barrier phenomenon in terms of the protein science.