The role of the GPI-anchor in prion disease pathogenesis is still a challenging issue. In vitro studies have shown that anchorless cellular prion protein (PrP(C)) undergoes aberrant post-translational processing and metabolism. Moreover, transgenic (Tg) mice overexpressing anchorless PrP(C) develop a spontaneous neurological disease accompanied with widespread brain PrP amyloid deposition, in the absence of spongiform changes. Generation of PrP forms lacking the GPI and PrP amyloidosis are striking features of human stop codon mutations in the PrP gene (PRNP), associated with PrP cerebral amyloid angiopathy (PrP-CAA) and Gerstmann-Sträussler-Scheinker (GSS) syndrome. More recently, the presence of anchorless PrP species has been also claimed in sporadic Creutzfeldt-Jakob disease (sCJD). Using a highly sensitive protein separation technique and taking advantage of reference maps of synthetic PrP peptides, we investigated brain tissues from scrapie-infected "anchorless PrP" Tg mice and wild type mice to determine the contribution of the GPI-anchor to the molecular mass and isoelectric point of PrP quasispecies under two-dimensional electrophoresis. We also assessed the conformational properties of anchorless and anchored prions under standard and inactivating conditions. These studies were extended to sCJD and GSS. At variance with GSS, characterization of PrP quasispecies in different sCJD subtypes ruled out the presence of anchorless prions. Moreover, under inactivating conditions, mice anchorless prions, but not sCJD prions, generated internal PrP fragments, cleaved at both N and C termini, similar to those found in PrP-CAA and GSS brain tissues. These findings show that anchorless PrP(Sc) generates GSS-like PrP fragments, and suggest a major role for unanchored PrP in amyloidogenesis.