The etiology of the autoimmune thyroid diseases (AITDs), Graves' disease (GD), and Hashimoto's thyroiditis (HT) is largely unknown. However, genetic susceptibility is believed to play a major role. The lymphoid tyrosine phosphatase (LYP), encoded by the protein tyrosine phosphatase-22 (PTPN22) gene, is a powerful inhibitor of T cell activation. Recently, a single-nucleotide polymorphism (SNP), encoding a functional arginine to tryptophan residue change at PTPN22 codon 620 in Caucasians has been shown to be associated with GD and other autoimmune diseases. We have used a polymerase chain reaction (PCR)-restriction fragment (XcmI) assay to examine genotypes at the codon 620 polymorphism in 334 unrelated patients with AITD and 179 controls. None of the patients with AITD and controls had the tryptophan allele. These data suggest that the codon 620 polymorphism of the PTPN22 gene does not have a causal role for AITD in the Japanese. However, we cannot exclude the PTPN22 region as harboring another susceptibility locus for AITD in linkage disequilibrium with the Trp/Arg SNP.