Factor V Leiden is the most common hereditary blood clotting disorder so far identified, with an allele frequency of 4%. The low prevalence of the mutation outside of Europe suggests it occurred as a single event in the European founding population. In this study four polymorphisms have been identified defining different haplotypes in the exon 13 region of the factor V gene. One of these polymorphisms predicts a novel amino acid change, threonine to serine, in the B-domain of factor V. Statistical evidence for a single origin of factor V Leiden is provided through the association of the mutation with a single exon 13 haplotype.