Disease-associated gene polymorphisms provide both scientific insight into pathophysiological mechanisms and clinical information regarding risk and progression. Of special interest is the epsilon4 allele of the apolipoprotein E gene, which has emerged as a substantial risk factor for late-onset forms of Alzheimer disease and also influences the risk of cardiovascular disease. Genotyping of apolipoprotein E can be performed by several methods; presented here are a quality and cost-benefit analysis of four different protocols on a cohort of 42 clinical samples is included in the unit. Each method resulted in genotyping with a high sensitivity and specificity. The newer microtiter-plate-based high-throughput techniques, fluorescence polarization and SNaPshot analysis, were as reliable as the traditional techniques of restriction fragment length polymorphism analysis and reverse hybridization. The reverse hybridization method tends to be more cost- and time-effective when the number of analyses is limited, although economy of scale favors fluorescence polarization or SNaPshot analysis in larger studies. The latter approaches also provide the flexibility to investigate other polymorphic disease markers.