CpG dinucleotides have been implicated as mutational hotspots in genes that are subject to control mechanisms involving methylation. We have used the polymerase chain reaction to amplify exons 2 and 6 of the human antithrombin III gene and direct sequencing to identify the base replacement in 12 genetic variants. These occurred in individuals with a history of thromboembolic disease due to functional abnormalities of circulating antithrombin: ten had decreased heparin binding and activation, two had decreased inhibitory activity. The amino acid abnormality in ten out of 12 cases had arisen at a CpG dinucleotide; this confirms the CpG sequence as a "hotspot" in the antithrombin gene and explains the observed frequency of occurrence of the same variant antithrombins in diverse populations.