Prekallikrein deficiency is a rare autosomal recessive disease not considered to be associated with a tendency for bleeding, despite marked prolongation of activated partial thromboplastin time. Currently, six kinds of mutations in the prekallikrein gene are known to be associated with prekallikrein deficiency. In this report, we describe a patient with idiopathic thrombocytopenic purpura who was recognized to have severe prekallikrein deficiency. Molecular analysis of the patient's prekallikrein gene showed a homozygous Trp499Stop nonsense mutation that has not been reported previously. The mutant allele is predicted to encode a truncated protein lacking half of the catalytic domain of prekallikrein, suggesting that the truncated protein causes prekallikrein deficiency in the patient.