It would be of clear interest and importance to identify T cell populations which correlate with the initiation of some T cell-mediated diseases; however, it is difficult to observe the initial response of T cells in these diseases because of modification due to immunosuppressive treatment. We investigated T cell receptor (TCR) V beta usage in both affected and unaffected mucosa from 16 patients with active Crohn's disease (CrD), undergoing nutritional therapy without any immunomodulatory medications. Semiquantitative reverse transcriptase-polymerase chain reaction showed increased expression of V beta 12 and 13 in the entire mucosa of CrD but not in the controls. This was confirmed by introducing a random cloning method. Such skewing was observed primarily in CD4+ lamina propria lymphocytes. DNA sequence analysis demonstrated a striking clonal expansion of V beta 12 T cells, but the dominant clones were not identical in the patients. These findings suggest the importance of superantigen as well as specific T cell response in the pathogenesis of CrD.