The development of B cell lymphoma, predominantly of the large-cell type, in patients with autoimmune diseases such as Hashimoto's thyroiditis or Sjogren's syndrome is well known. In Sjogren's syndrome, it has been recently shown that the benign-appearing lymphocytic infiltrates of the lymphoepithelial lesions in the salivary glands have clonal rearrangements of immunoglobulin genes in their DNA, even in the absence of malignant lymphoma. To investigate whether a similar situation occurs in Hashimoto's thyroiditis, we studied the thyroid glands from four patients with this disease. In all four cases, there was a benign-appearing lymphocytic infiltrate in the thyroid, with eosinophilic changes in the Hurthle cells. In immunologic studies, we determined that the lymphocytes were polyclonal in each case. We extracted DNA from the frozen tissue blocks of these four patients and analyzed it by molecular hybridization for the presence of clonal immunoglobulin (IgH, kappa, and lambda) and T cell receptor beta chain gene rearrangements, and detected none in any case. Therefore, we conclude that the lymphocytes in Hashimoto's thyroiditis are immunologically and immunogenetically polyclonal proliferations of cells, and that the initial lesion of Hashimoto's thyroiditis does not contain a detectable clone of cells that may eventually develop into malignant lymphoma.