Methylation of the proximal promoter of the ABL1 oncogene is common epigenetic alteration associated with clinical progression of chronic myeloid leukemia (CML). In presented study we queried whether both the Ph'-associated and normal ABL1 alleles undergo methylation; what may be the proportion of hematopoietic progenitors bearing methylated ABL1 promoters in chronic versus acute phase disease; whether methylation affects the promoter uniformly or in patches with discrete clinical relevance; and, finally whether methylation of ABL1 reflects a generalized process or is gene-specific. To address these issues, the technique of methylation-specific PCR and bisulfite-sequencing was adapted to study the regulatory regions of ABL1 and other genes. In cell lines established from CML blast crisis, which only carry a single ABL1 allele nested within the BCR-ABL fusion gene, ABL1 promoters were universally methylated. In clinical samples from patients at advanced stages of the disease, both methylated and unmethylated promoter alleles were detectable. In colonies derived from single hematopoietic progenitors methylated and unmethylated promoter alleles were revealed as well. ABL1 methylation was was noted in the vast majority of colonies from blast crisis, but not chronic-phase CML. It was shown finally that ABL1 methylation does not reflect a generalized process and may be unique among DNA repair/genotoxic stress response genes. These data suggest that specific methylation of the Ph'-associated ABL1 allele accompanies clonal evolution in CML.