Despite the frequent description of 6q- structural abnormalities in human leukemias and lymphomas, rearrangements of the c-MYB locus have not been detected. We have detected a rearrangement in the c-MYB proto-oncogene in the cell line CCRF-CEM, an immature T-cell leukemia cell line which is not 6q-. Due to this rearrangement, a large portion of the c-MYB promoter conserved between the human and murine c-MYB genes is lost. The rearranged locus, which we have designated MRR (MYB rearranged region), has been cloned and mapped to chromosome 6. Field inversion gel electrophoresis (FIGE) studies reveal that the MRR sequence is linked to the c-MYB locus, suggesting that the rearrangement is due to a submicroscopic deletion. The rearrangement appears to have no effect on c-MYB promoter activity as analyzed in CCRF-CEM cells. The normal locus of the MRR sequence has been cloned from a human placental genomic library. Partial sequence analysis of this clone reveals that a portion of the DNA lost in the rearrangement shows a high degree of homology to a member of the myc family of oncogenes. Thus the characterization of this rearrangement has yielded a new set of probes for the study of chromosome 6q abnormalities in human leukemias and lymphomas and provides the first evidence for potential involvement of the c-MYB locus itself in submicroscopic deletions within chromosome 6.