The Philadelphia chromosome, t(9;22), is present in virtually all cases of chronic myeloid leukemia (CML). It has previously been shown by cytogenetic studies that the rearranged chromosome 22 in patients with CML is exclusively maternal in origin. To address this issue at a molecular level, the major breakpoint cluster region (M-bcr) on chromosome 22 was examined using Southern blot assays and M-bcr Pvu II and Mae II restriction site polymorphisms in three CML patients. In all three cases, the rearranged allele was paternal in origin. These results indicate that the paternally derived M-bcr allele may also be involved in the M-bcr rearrangement.