Prions are abnormal conformers (PrPSc) of the host-encoded cellular prion protein (PrPC). They replicate by templating the conversion and polymerization of PrPC. Multiple strains of prions are recognized phenotypically within the same host species. Prion strains exhibit specific incubation periods, stereotyped clinical signs and neuropathology, and specific tropism for the cerebral and lymphoid tissues. Strains are conformational variants of PrPSc at the level of the tertiary and/or quaternary structure. This usually results in one dominant PrPSc conformation as detected by conventional immunodetection methods, although there is evidence that prions can be composed of several substrains. Substrain selection is expected to occur during adaptation of a prion to a new host: differences in recipient PrP primary sequence are supposed to drive modifications of the conformational rearrangements of the native PrP in order to fit the inoculum. The efficacy of this process differs between the brain and lymphoid tissue, sometimes resulting in a lowered species barrier in the lymphoid tissue. By using transgenic animals expressing PrP at variable levels, we also showed that substrain selection occurred during homotypic transmission events and is controlled by variations in the expression level of host PrP in the brain. The question then arises of similar substrain selection within different tissue of the same infected host due to variations in PrP expression levels, e.g. central nervous system vs. other peripheral organs such as the lymph nodes or the spleen. We will here present data supporting the view that PrPC expression levels are instrumental in prion substrain selection and specific tropism for the lymphoid tissue. These results highlight the importance of screening prions in other organs than the central nervous system to apprehend prion diversity and potential of evolution.