Malignant non-Hodgkins lymphoma with primary involvement of the thyroid is a rare disease. Nearly all these lymphomas are of B-cell phenotype, and they represent a broad morphological spectrum of high and low grade entities. We investigated 18 cases of Hashimotos disease and 95 cases of thyroid non-Hodgkins lymphoma including 16 cases of MALT-lymphoma. This type of lymphoma is often hardly distinguishable from reactive lesions, even by immunohistochemistry. Therefore, we introduced a new molecular genetic technique based on the polymerase chain reaction (PCR) combined with temperature-gradient gel electrophoresis to demonstrate monoclonal populations of B cells in a polyclonal background of reactive B lymphocytes. With this approach we found monoclonality in 4 of 18 cases of Hashimotos disease. In our opinion, these 4 cases demonstrate clearly the transition from autoimmune disease into non-Hodgkins lymphoma.