A previous patho-epidemiological study indicated that thyroid lymphoma (TL) evolves among active lymphoid cells into chronic lymphocytic thyroiditis (CLTH), a thyroid-specific autoimmune disease. In this study, clonality of B-cells in the CLTH and TL lesions was analyzed using polymerase chain reaction (PCR)-based method on surgically resected samples from 10 cases of TL; 7 mucosa-associated lymphoid tissue (MALT) lymphoma and 3 diffuse large B-cell lymphoma (DLBCL). CLTH lesions coexisted in all the cases with MALT lymphoma, but not in the three DLBCL cases. In cases of MALT lymphoma, the lymphomatous and CLTH areas were separately microdissected from each section and analyzed for clonality. In the cases of DLBCL, the whole specimens were used for clonality analysis. CLTH lesions showed smear in 6 samples, two bands in one, and more than three (oligoclonal pattern) in 2. MALT lymphoma lesions showed single or two bands (monoclonal pattern) in 4, oligoclonal pattern in 4, and smear in one. DLBCL showed monoclonal pattern in two and oligoclonal pattern in one. One common band was present among two separate MALT lesions in one case, but no common bands were found in the remaining six cases. These findings suggested the clonal evolution of B-cell from polyclonal to monoclonal proliferation to take place in the continuum of lymphoproliferative lesions into autoimmune thyroiditis.