Biopsies of various tissues from eight patients with confirmed cutaneous T-cell lymphoma were analyzed for lymphomatous involvement using V-J junctional sequences in rearranged T-cell receptor-gamma genes as specific molecular markers for the malignant clone. The patients included one stage IA, one stage IB, and six stage IVA. Twenty-five specimens were analyzed including 14 skin, five lymph node, four blood, and two bone-marrow samples. Ten skin samples and four lymph node samples were histologically positive for lymphoma. The other specimens were morphologically uninvolved. An assay involving polymerase chain reaction (PCR) amplification of T-cell receptor-gamma gene rearrangements and denaturing gradient gel electrophoresis was used to identify the tissue specimen containing the greatest tumor clone density in each case. This specimen was then used to generate a tumor-specific RNA probe that was used to molecularly stage each patient by means of an assay involving PCR gene amplification and RNase protection analysis (PCR/RPA). This assay detected malignant cells in all available biopsies, including morphologically uninvolved extracutaneous tissue samples (two blood, one lymph node, and one bone marrow) obtained from the two patients in pathologic stage I. Microscopic examination and the less sensitive PCR/denaturing gradient gel electrophoresis technique failed to detect lymphomatous involvement in 11 (44%) and eight (32%) of these 25 specimens, respectively. We conclude that molecular biologic staging using PCR/RPA is able to demonstrate morphologically occult dissemination of cutaneous T-cell lymphoma in early disease. In addition, PCR/RPA may be able to monitor tumor response to therapy and detect early recurrence of malignant lymphomas during clinical remission.