Detection of a clonal T cell receptor (TCR) gene rearrangement is used in the diagnosis of primary cutaneous T cell lymphomas (CTCL) whereas chromosomal aberrations serve as a diagnostic tool for leukaemias and nodal lymphomas. To what extent both approaches specify the same cell population remains unknown. We investigated the coincidence of TCR clonality with complex clonal chromosomal aberrations, indicating qualitative alteration of the affected cells, in 17 CTCL patients. Out of 41 skin, blood, and lymph node samples studied, 34 gave results in chromosome and TCR analyses. With 88%, most specimens revealed corresponding results by both techniques (27 of 34 clonal, three of 34 non-clonal). In two patients, analysis of micro-dissected cells demonstrated that neoplastic T cells bear both a dominant TCR rearrangement and a complex chromosomal aberration. The cutaneous clone was found in blood samples of 11 of 12 patients (including early stages), and investigation of follow-up skin and blood samples indicated persistence of the T cell clone in 11 of 14 cases. In conclusion, we show that dominant TCR clones and chromosomal clones converge in all stages of CTCL. These clones disseminate into blood and skin at early disease stages and persist despite therapy. The coexistence of a dominant TCR clone and a clonal chromosomal aberration can thus be used as a hallmark of malignancy.