The 8;21 translocation is one of the most common specific rearrangements in acute myelogenous leukemia. We have Identified markers (D21S65 and aNotI boundary clone, Not-42, referred to as probe B) flanking the chromosome 21 translocation breakpoint (21q22.3) that demonstrate physical linkage in normal genomic DNA, by using at least three restriction endonucleases (Not I, Sac a, and BssHl), and that are located not more than 250-280 kilobases apart. Pulsed-field gel analysis of DNA from somatic cell hybrids containing the 8;21 translocation chromosomes demonstrates rearrangement of these markers. A 470-kilobase yeast artificial chromosome, YAC-Not-42, has been isolated that contains both probes.Mapping of A subelones constructed from YAC-Not-42 suggests that >95% (25/26 probes tested) of the yeast artificial chromosome DNA is located on the proximal (D21S65) side of the breakpoint. In situ hybridization studies using metaphase chromosomes from five acute myelogenous leukemia patients with the 8;21 trandocation confirmed these results and demonstrated the translocation of probe B to the derivative chromosome 8. A chromosome walk of w39 kilobases from probe B has allowed identification of the breakpoint in DNA from a somatic cell hybrid conining the derivative chromosome 8. Since probe B contains conserved DNA sequences and is in dose proximity to the translocation breakpoint, it may represent a portion of the involved gene on chromosome 21.