Tyrosine kinase inhibitors (TKI) have significantly improved the prognosis for chronic myelogenous leukemia (CML) patients. Several mechanisms of resistance have been identified, however. BCR-ABL-dependent resistance is the most frequently occurring, usually as mutations preventing therapeutic drug interaction. This study addresses a mechanism of resistance observed in the absence of mutations. During TKI challenge, of downstream dephosphorylators such as Protein-Tyrosine Phosphatase, Nonreceptor-Type 6 (PTPN6 or SHP1) may supplement oncogenic activation. We retrospectively examined expression and control of SHP1 in TKI sensitive and resistant cases of CML in 122 North American patients of European and African ancestry employing mutation detection, methylation analysis and gene expression. Mean SHP1 gene expression was lower in CML cases (SHP1/beta2 microglobulin% = 399.4) than in nonleukemic samples (SHP1/beta2 microglobulin% = 704.5). Mutations were detected in 16/28, 26/47 and 5/18 of TKIresistant cases by standard PCR, quantitative PCR and sequencing, respectively. Expression of SHP1 was slightly lower in cases of drug-resistant CML than in drug sensitive CML (SHP1/beta 2 microglobulin% = 382 vs 422). Methylation of the SHP1 promoter at CpG site at -456 was significantly higher in cells from CML patients than in cells from normal patients (p=0.023). Depressed expression and increased methylation of SHP1 in CML cells are consistent with a role of tumor suppressor of SHP1, with its loss contributing to malignant cellular phenotypes. Although no significant differences were observed in SHP1 expression and methylation in TKI-resistant and TKI sensitive CML, expression was consistently lower and methylation higher in cases of TKI-resistant CML without detectable ABL kinase mutations. Methylation as the cause of SHP1 (or other tumor suppressor gene) suppression would offer new therapeutic strategies for treating CML.