Mammalian prions (PrPSc) consist of misfolded, conformationally altered, self-replicating states of the sialoglycoprotein called prion protein or PrPC. Recent studies revealed that the sialylation status of PrPSc plays a major role in evading innate immunity and infecting a host. Establishing the type of linkage by which sialic acid residues are attached to galactose is important, as it helps to identify the sialyltransferases responsible for sialylating PrPC and outline strategies for manipulating the sialyation status of PrPSc. Using enzymatic treatment with sialidases and lectin blots, the current study demonstrated that in N-linked glycans of PrPSc, the sialic acid residues are predominantly 2,6-linked. High percentage of 2,6-linked sialic acids were observed in PrPSc of three prion strains 22L, RML and ME7, as well as PrPSc from brain, spleen or N2a cells cultured in vitro. Moreover, the variation in the percentage of 2,3- versus 2,6-linked sialic acid was found to be relatively minor between brain-, spleen- or cell-derived PrPSc, suggesting that the type of linkage is independent of tissue type. Based on the current results, we propose that sialyltransferases of St6Gal family, which is responsible for attaching sialic acids via 2,6-linkages to N-linked glycans, controls sialylation of PrPC and PrPSc.