Use was made of allele-specific PCR to develop a highly effective DNA diagnostic system for detection of the factor V Leiden mutation in exon 10 of human factor V gene. The allele-specific primers contain a 3'-OH end nucleotide, which matches a mutant or wild-type nucleotide of the template DNA (A-allele and G-allele, respectively) and also one mismatched nucleotide near the 3'-end. The universal primers have an internal mismatch with the mutant nucleotide of the template DNA and another mismatched nucleotide at 3'-OH end. The A-allele-specific primer enables the preferential amplification of both the homozygous and heterozygous mutant alleles. The extension of the G-allele-specific primer or the universal one is inhibited in the presence of the homozygous factor V Leiden. The developed assay system allowed us to detect five patients, who are heterozygous for factor V Leiden among the 48 patients with deep venous thrombosis and pulmonary thromboembolism.