During the development of T lymphocytes, the noncontiguous germline V(D)JC segments are rearranged to generate functional receptor polypeptides on the cell surface, and the pattern of T-cell receptor (TCR) gene rearrangement can provide a highly sensitive marker for clonality, cell lineage and diagnosis of lymphoid neoplasms. We analysed 3 cases of SLE, 5 cases of Hashimoto`s thyroiditis and 8 cases of malignant lymphomas for the presence of TCR gene rearrangements. The TCR-β gene was rearranged in both B and T lymphomas. Although rearrangements of the TCR-β gene in the lymphomas provide a valuable clinical marker, cell lineage can not be assigned by the rearrangement patterns. The TCR-γ gene was not rearranged in lymphomas, possibly due to the limited population of the γδ-T cells in the tumor tissues. However, rearrangements of the TCR-γ gene were detected in all cases of SLE and Hashimoto`s thyroiditis, suggesting that rearrangements of the TCR-γ gene may be implicated in the pathogenesis of certain autoimmune disease.