A microdeletion on the derivative chromosome 9 (der(9)) formed by the Philadelphia translocation, has been identified in 10--20% of CML patients and results in a poor prognosis. Haploinsufficiency of one or more genes in the deleted region could alter chronic myeloid leukemia (CML) oncogenesis leading to more aggressive disease. Alternatively, the presence of this deletion may be indicative of an intrinsically unstable genome and a disease phenotype with a greater adaptive response. Microarray comparative genomic hybridization (aCGH) allows for a high-resolution interrogation of the entire genome in a single experiment. aCGH of CML patients with a deletion on the der(9) resulted in the identification of a new DNA polymorphism on chromosome14, a large-scale copy number polymorphism (CNPs), called CNP14q12. CNP14q12 was shown to occur more frequently in DNA samples from cancer patients than in cytogenetically normal individuals (p < 0.01). This suggests that molecular mechanisms that govern genome stability may be associated with both acquisition of the CNP14q12 polymorphism and an increased susceptibility to undergo complex genomic rearrangements such as der(9) deletion. The identification of this CNP in CML highlights the need for increased research into the composition of the genome, as well as the factor(s) resulting in the poor prognosis seen in CML patients with a deletion on the der(9) chromosome.