We have analyzed genomic DNAs from a patient who developed acute myeloid leukemia 1 year after a myeloproliferative disorder was diagnosed. The development of the acute leukemia was associated with the acquisition of a t(9;11)(p22;q23) chromosome translocation. ALL-1 gene rearrangement, on chromosome 11, was present at the onset of the acute phase, but not during the chronic phase of the myeloproliferative disorder. The genomic rearrangement on chromosome 9 was within an unidentified region. By the use of polymerase chain reaction, we were able to determine that the chromosomal rearrangement was completely absent during the chronic phase of the myeloproliferative disorder, indicating that the ALL-1 gene rearrangement was causally related to the development of the acute phase. The rapid progression into the acute phase suggests that this case might be therapy related. This work provides a clear example of association of a molecular defect with the development of a specific clinical leukemic stage, and supports the indication that ALL-1 gene rearrangement is associated with poor clinical outcome in adult leukemias.