Follicular lymphomas are often associated with t(14;18) chromosomal translocation. The rearrangement site (bcl-2/JH junctional region) between the two chromosomes is hypervariable regarding its size and DNA sequence, and is a potential specific marker for the neoplastic clone of each patient. We report the use of the polymerase chain reaction (PCR) technique for detecting and sequencing clonal bcl-2/JH rearrangements in lymph nodes and/or bone marrow specimens from patients with follicular lymphoma. 53 patients at diagnosis (n = 40) or at relapse (n = 13) were studied. 25 of these 53 cases were found to have the t(14;18) translocation involving either the major breakpoint region (MBR) (n = 21) or the minor cluster region (mcr) (n = 4). Since our PCR technique could detect the translocation in 1/10(6) cells we had to distinguish malignant cells from possible t(14;18)-bearing non-malignant cells which could be present during and after treatment. The bcl-2/JH junctional regions were therefore sequenced in order to synthesize an anti-junction oligonucleotide probe specific for each patient's malignant clone (clonospecific probe). Using these clonospecific probes for hybridization it was possible to detect one malignant cell mixed with 10(6) normal cells. 28 patients with advanced stage (stage III and IV), had been enrolled for treatment with myeloablative chemoradiotherapy and autologous bone marrow transplantation (ABMT). In 12 of these patients bcl-2/MBR translocation was found at diagnosis and used as a marker to detect the presence of residual lymphoma cells in serial bone marrow (BM) and peripheral blood (PB) samples. In three relapsed patients (with available tissue samples at diagnosis and relapse), clonospecific probes clearly demonstrated the same bcl-2/JH junction, thus confirming that the relapse occurred from the same malignant clone, and which remained stable without any clonal evolution of its junctional region throughout the course of the disease. These results demonstrate the value of the t(14;18) clonospecific probes as a diagnostic tool in the detection of minimal residual disease and relapses in patients with follicular lymphoma.