The human prion diseases (spongiform encephalopathies) Creutzfeldt-Jakob disease (CJD) and Gerstmann-Sträussler syndrome (GSS), are neurodegenerative disorders characterised by the accumulation of an abnormal isoform of the prion protein. The normal prion protein is a phosphatidyl inositol anchored, membrane bound sialoglycoprotein of widespread tissue distribution but expressed predominantly in the brain. 15% of prion diseases are autosomal dominant genetic disorders associated with mutations in the gene encoding the prion protein. To date six pathogenic amino acid substitutions have been identified in affected family members, in addition to five distinct insertional events which occur within a region of the protein comprising four tandem octapeptide repeats. We have investigated deletions within this region and have identified three specific deletions. We report here that these deletions are not associated with CJD and represent a new class of polymorphism within the prion protein gene.