Polymorphisms of the gene encoding apolipoprotein E have been implicated in the pathogenesis of peripheral and coronary artery disease and neurodegenerative disorders such as sporadic and late-onset familial forms of Alzheimer's disease. We have developed TaqMan assay systems for the single nucleotide polymorphisms -219G/T, located in the promoter of the apolipoprotein E gene, 113G/C, present in the transcriptional enhancer element of intron 1, 334T/C, determining Cys or Arg as amino acid residue 112 of mature apolipoprotein E, and 472C/T, determining Arg or Cys as residue 158. The accuracy of genotype determination with the TaqMan systems was demonstrated by analyses with restriction endonucleases. We determined the genotypes of the apolipoprotein E polymorphisms in 2349 study subjects. The genotypes were distributed as: -219GG = 27.3%, -219GT = 49.1%, and -219TT = 23.6% (p = 0.435); 113GG = 41.3%, 113GC = 45.2%, and 113CC = 13.5% (p = 0.343); 334TT = 73.4%, 334TC = 24.7%, and 334CC = 1.9% (p = 0.539); 472CC = 86.3%, 472CT=12.8%, and 472TT= 0.9% ( p = 0.004) (Hardy-Weinberg equilibrium estimates are given in parentheses). The allele combinations which define the three major isoforms of apolipoprotein E, namely apoE2, apoE3, and apoE4, had the following allele frequencies: 334T/472T (epsilon2; 112Cys/158Cys) = 7.3%, 334T/472C (epsilon3; 112Cys/158Arg) = 78.4%, and 334C/472C (epsilon4; 112Arg/158Arg) = 14.2%, respectively. ApoE genotypes were distributed as: epsilon2epsilon2 = 0.9%, epsilon2epsilon3 = 11.2%, epsilon2epsilon4 = 1.6%, epsilon3epsilon3 = 61.3%, epsilon3epsilon4 = 23.1%, and epsilon4epsilon4 = 1.9% (p = 0.014). The TaqMan assays allow for fast and sensitive genotyping and are especially suitable for studies including large numbers of participants.