Recent advances in genotyping techniques and genomic knowledge via the Hap Map and Human Genome projects allow for true Genome-Wide Association (GWA) analysis for common complex diseases such as heart disease, diabetes, and Alzheimer's. A major obstacle in GWA analysis is the prohibitively high cost of genotyping the possibly thousands of individuals necessary to achieve statistical significance of results. One potential solution is to pool the DNA of case and control populations and to determine the genotype allele frequency differences in these populations by pooled allelotyping. While pooling can dramatically save time and money, it also adds sources of error. Our work has created a system process that allows for direct evaluation and comparison of pooled allelotyping to individual genotyping for GWA association analysis of complex disease.