Transmissible spongiform encephalopathies (TSE) are characterised by the accumulation in the central nervous system of the abnormal form of the prion protein (PrPTSE). The mechanism underlying the pathological conversion of the PrP and the role played by other factors are still under investigation. Genetic forms of human TSEs are associated with mutations along the PrP sequence; it is still not clear whether the presence of the altered residue plays a role in the mechanism of the pathological conversion: it could only be involved in the start of the transformation, for example by enhancing the affinity for a molecular trigger, or it could destabilise the PrP and render the protein more incline to acquire the abnormal conformation. In this latter scenario the mutant PrP would be converted at a significantly higher level than the wild type allotype. In this study, a quantitative analysis of the PrPTSE allotypes accumulated in the frontal brain cortex of a familial Creutzfeldt-Jakob disease affected patient carrying the R208H mutation has been performed by the use of mass spectrometric techniques. The stoichiometric ratio of the two allotypes has been determined through the use of calibration curves set up by means of opportune synthetic peptides and internal standards. We found that the quantity of the mutant allotype is higher than the wild type counterpart, nevertheless the mutant/wild type ratio is lower than 5/1. These results suggest that the presence of the R208H mutation is involved in favouring the pathological conversion of PrP and are in agreement with the data obtained with recombinant PrP (Apetri A.C. et al. J. Biol. Chem., 2004) which show that the R208H mutation may destabilise the alpha-helix structured protein. It is still to be evaluated whether the presently detected stoichiometric ratio is significant for the determination of the precise role of the mutant protein: further investigations are being set up in order to elucidate this important issue.