A comparative semi-automated morphometric study was performed on the distribution of prion protein, spongiform change and astrocytosis in the brains of nine cases of sporadic Creutzfeldt-Jakob disease of differing genotype at the methionine-valine polymorphism at codon 129 of the prion protein gene. Custom-designed image analysis software was used to produce objective figures for each of the different pathological features throughout 13 different areas of the brain used for analysis. A significant positive correlation was observed between prion protein deposition and astrocytosis in all cases and no significant correlation was observed between spongiform change and prion protein deposition. Different patterns of pathology were found to relate to codon 129 genotype; valine homozygosity favoured the targeting of pathology to deep grey matter structures, while methionine homozygosity favoured cortical targeting of pathology. These results provide evidence that prion protein deposition is closely associated with an astrocytic reaction and suggest that codon 129 genotype may influence the pathological phenotype.