The agents responsible for transmissible spongiform encephalopathies (TSEs), or prion diseases, contain as a major component PrP^Sc, an abnormal conformer of the host glycoprotein PrP^C. TSE agents are distinguished by differences in phenotypic properties in the host, which nevertheless can contain PrP^Sc with the same amino‐acid sequence. If PrP alone carries information defining strain properties, these must be encoded by post‐translational events. Here we investigated whether the glycosylation status of host PrP affects TSE strain characteristics. We inoculated wild‐type mice with three TSE strains passaged through transgenic mice with PrP devoid of glycans at the first, second or both N‐glycosylation sites. We compared the infectious properties of the emerging isolates with TSE strains passaged in wild‐type mice by in vivo strain typing and by the standard scrapie cell assay in vitro. Strain‐specific characteristics of the 79A TSE strain changed when PrP^Sc was devoid of one or both glycans. Thus infectious properties of a TSE strain can be altered by post‐translational changes to PrP which we propose result in the selection of mutant TSE strains.