A novel mutation in the 3' untranslated region of the prothrombin gene, prothrombin 20210A, recently has been identified. This mutation is associated with increased serum prothrombin levels and an increased risk for venous thromboembolism. Patients who carry a mutation in the factor V gene (factor V Leiden) have also been demonstrated to be at increased risk for venous thromboembolism, and previous studies have identified a population prevalence of approximately 5% to 10% for the factor V Leiden allele. To simply and reliably identify patients who carry both genetic defects, a novel assay was developed that simultaneously determines the genotype of patients for the factor V Leiden allele and the prothrombin 20210A mutation. Representative samples (samples positive and negative for each mutation and a "double mutant") were then subjected to this single-tube genotyping assay. The results indicate that the simultaneous genotyping of these mutations will readily characterize the allelic status of patients for the two most frequent genetic mutations in the coagulation cascade.