The BCL6 gene is frequently altered by chromosomal translocations and/or point mutations at its 5' non-coding portion in B-cell non-Hodgkin's lymphoma (B-NHL). We analysed submicroscopic structural alterations of the BCL6 gene which had arisen from internal deletion in four cases with B-NHL and found that these deletions overlapped at the 280 bp region in the first intron. In electrophoretic mobility shift assay, nuclear extracts prepared from various cell lines were shown to bind to a fragment from this commonly deleted region. Our results suggest that deregulation of BCL6 expression would be caused by loss of this putative protein-binding sequence in some B-NHL cases.