Distinguishing between thyroid malignant lymphoma and lymphocytic thyroiditis (Hashimoto's thyroiditis) is quite difficult and problematic. Molecular techniques to detect clonal lymphoid proliferation based on Ig heavy chain (IgH) gene rearrangement may be used to facilitate more accurate diagnosis of malignant lymphoma. We recently established a method for diagnosing thyroid tumors by analyzing ribonucleic acids (RNAs) extracted from the needles used for fine needle aspiration biopsy (aspiration biopsy-RT-PCR). By applying the aspiration biopsy-RT-PCR method to detection of the monoclonality of IgH messenger RNA (mRNA), an accurate molecular-based diagnosis of malignant lymphoma can be established as an adjunct to cytological diagnosis. We first studied RNAs from fresh tissues samples of 8 cases of Hashimoto's thyroiditis and 18 malignant lymphomas to detect the monoclonality of IgH mRNA by seminested RT-PCR. Monoclonality was detected in 8 of 18 (44.4%) malignant lymphomas, but in none of the 8 cases of Hashimoto's thyroiditis. We then studied aspirates from 10 cases of thyroid malignant lymphoma, 4 cases of Hashimoto's thyroiditis, and 1 case each of adenomatous goiter and papillary carcinoma. Monoclonality was detected in the aspirates from 4 of 10 malignant lymphomas (40%), but not from other tissues. Thus, RT-PCR detection of monoclonality of IgH mRNA in addition to cytological examination may be useful in diagnosing thyroid malignant lymphoma.