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Factor V Leiden is the most common genetic risk factor for thrombosis. Currently, the determination of factor V Leiden genotype is limited to laboratories with expertise in molecular methods to develop “home brew” assays using polymerase chain reaction (PCR) to amplify genomic DNA, followed by analysis of Mnl I restriction fragments. These methods are not standardized, are labor intensive, and have low throughput. We describe a method for determination of factor V Leiden genotype using allele-specific oligonucleotide capture probes coated onto 96 well plates, requiring only a thermal cycler and a microplate spectrophotometer to perform. With an automated strip washer and plate reader, genotypes could be determined in 80 min from completion of PCR. Within-run and between-run coefficients of variation for the assay were <10%. In all 160 cases studied, the microplate assay correctly identified the factor V genotype. The microplate oligonucleotide hybridization assay is a simple and reliable system for determination of factor V Leiden genotype. The assay offers an automatable, high-throughput alternative to current testing methodologies.