Apolipoprotein E (apoE) allele epsilon4 is a major risk factor for Alzheimer's disease (AD); however, the molecular mechanism underlying the acceleration of the development of AD in patients possessing epsilon4 remains to be determined. To investigate the isoform-specific effects of apoE on neurons, primary neuron cultures were prepared from fetal rat cerebral cortices. Inhibition of de novo cholesterol synthesis by compactin, a 3-hydroxyl-3-methylglutaryl CoA reductase inhibitor, induced neuronal cell death in a dose dependent manner. In the presence of a sublethal dose of compactin, apoE4 with beta-migrating very low density lipoproteins (beta-VLDL) caused apoptotic cell death in neuronal cultures. The same results were obtained with inhibition of de novo cholesterol synthesis by sublethal doses of squalestatin, an inhibitor of squalene synthase. The de novo cholesterol synthesis was suppressed to a higher degree by apoE4 than by apoE3, administered with beta-VLDL in the presence or absence of compactin. Mevalonate and squalene, which are metabolites of the cholesterol synthesis pathway, protected neuronal cells from apoE4-induced cell death. These results may suggest that apoE4 may exhibit neurotoxic action when de novo cholesterol synthesis is suppressed to a certain level, and that apoE4 induces neuronal cell death through the suppression of de novo cholesterol synthesis via an undetermined isoform-specific mechanism.