BCL6 translocations involve not only immunoglobulin (IG) genes but also a number of non-IG loci as partners. Junctional sequences of three IG/BCL6 translocations were readily obtained by long-distance PCR. In cases where partner loci were not determined, we developed a long-distance inverse PCR method, which amplifies unknown fragments flanked by known BCL6 sequences. Using these two long-distance PCR-based approaches, we cloned junctional areas of BCL6 translocations from a total of 58 cases of B-cell tumors. Nucleotide sequencing and database searches revealed that 30 cases involved IGs as partners: IG heavy chain gene in 22, IG kappa light chain gene in 1, and IG lambda light chain gene in 7. In contrast, 23 cases affected non-IG loci, including the H4 histone gene, heat shock protein genes HSP89alpha and HSP90beta, and PIM-1 proto-oncogene. On der(3) chromosomes, complete sets of the promoters of these partner genes replaced that of BCL6 in the same transcriptional orientation. These results suggest that BCL6 gene affected by the translocation is transcriptionally activated by a variety of stimuli, including cell cycle control, changes in the physical environment, and response to cytokines. Break points on BCL6 occurred within the major translocation cluster, and we identified a 120-bp hyper-cluster region a short distance from the 3' end of exon 1. Gel mobility-shift assay suggested the presence of a protein(s) that bound to this particular region.