A series of expression microarray analyses of chronic myeloid leukemia (CML) by means of complementary DNA microarray representing a set of 1024 human genes were initiated to evaluate the role of expression microarray analysis in CML and to identify CML-associated genes. Among the target genes, 388 differentially expressed genes were identified. In 2 cases the expression level of 74 to 91 genes and in 3 cases that of 45 genes differed between the normal control and CML cells. Results of analysis of messenger RNA profiles indicated that 19 of 45 differentially expressed genes were up-regulated whereas others were down-regulated. The expression profile included oncogenes, tumor suppression genes, and human genes encoding proteins involved in the functions of transcription, signal transduction, metabolism, cell growth, differentiation, and apoptosis. The function of the immune system also was observed. Identification of these genes allows a quantitative view of the changes that accompany CML at the genomic level and enables deeper insights into the molecular basis of the disease.