Inheritance of the epsilon4 allele of apolipoprotein E (APOE, gene; apoE, protein) represents the most common genetic risk factor for developing Alzheimer's disease (AD), but the role of apoE in AD pathogenesis is yet to be clarified. A number of studies investigating apoE expression and protein levels in AD brain in correlation to its genetic polymorphism has yielded controversial results. We designed our approach based on neuropathological characteristics of AD to investigate apoE levels in relation to the APOE genotype and AD-related neurofibrillary changes, and amyloid deposits. We determined hippocampal apoE levels by reducing sodium dodecylsulfate-polyacrylamide gel electrophoresis and immunoblotting in 70 Braak-staged and APOE-genotyped autopsy brains. In our stage-, age- and gender-matched case sample, we found a significant increase of hippocampal apoE in the APOE epsilon3 homozygotes with beginning AD-related pathology (Braak stages I and II) compared with brain samples free of neurofibrillary changes and amyloid deposits. In the APOE epsilon4 allele carriers no such increase was found. In both genotype groups, severely affected brain samples with widespread neurofibrillary changes (Braak stages V and VI) and amyloid deposits (Braak stage C) showed low apoE levels comparable to those found in unaffected brain samples (Braak stage 0). Our data suggests that the isoform-specific impact of apoE on the development of AD may be of crucial importance only in the early stages of the disease. These stages are believed to represent phases of the disease in which the beginning neurodegeneration can be compensated by plastic reorganization.