TSE strains are routinely identified by their incubation period and vacuolation profile in the brain after intracerebral inoculation and serial passaging in inbred mouse lines. There are some major drawbacks to this method that are related to the variation in vacuolation that exists in the brains of mice infected with the same TSE strain and to variation between observers and laboratories in scoring vacuolation and determining the final incubation period. Aim: We investigated the potential of PrPSc immunohistochemistry and triplex Western blotting as possible alternative methods to differentiate between TSE strains. Methods: TSE reference strains ME7, 87A/87V, 22A/22C, 79A/79V and 301C/301V were intracerebrally inoculated in RIII or VM inbred mice that differ in their PrP genotype. Immunohistochemical PrPSc profiles were drawn up by scanning light microscopy both on coronal and sagittal sections. Results: On the basis of the localization of PrPSc in the cerebral cortex, hippocampus, and cerebellar cortex and the overall type of PrPSc staining, all TSE strains could be well differentiated from each other through their typical strain dependent characteristics. In addition, Western blot showed that the combination of glycosylation profile and 12B2 epitope content of PrPSc allowed to distinguish between all reference strains except for ME7 and 22A in VM mice. Conclusion: TSE strains in mice can be identified on the basis of their PrPSc profile alone. The potential to identify TSE strains in ruminants with these PrPSc profiles after a single primary passage in mice will be the topic of future studies.