Chronic myeloid leukemia (CML) is a clonal disease from hematopoietic stem cells.Surviving leukemia st em cells (LSCs) and progenitor cells are a potential source for CML relapse and progression.Recent data reported t hat IL-1 receptor accessory protein (IL1RAP) gene was differentially expressed in CML versus normal stem and pr ogenitor cells.However, whether the level of IL1RAP is associated with clinical phases of CML, and correlations b etween IL1RAP expression and detections of diagnosis is still unclear.Here we demonstrated that IL1RAP was up-regulated in CD34+ and CD34+CD38-cells which highly enriched with stem cells.Furthermore, IL1RAP expression in CD34+CD38-cells was tightly consistent with the generation of BCRABL fusion gene and philadelphia chromosome.Importantly, we found that the level of IL 1 RAP increased with dise ase progression from chronic phase (CP) into accelerated phase (AP) and blast phase (BP), which was investigated n ot only in new diagnosed CML patients but also in patients treated with tyrosine kinase inhibitors (TKI) and hydroxy urea.Negative correlation was detected between IL1RAP expression and neutrophil (NE), whereas no relation was f ound in white blood cell (WBC), lymphocyte (LY), red blood cell (RBC), platelet (PLT), age or gender of CML patie nts.In conclusion, we identified IL1RAP as a surface marker of LSCs may be a potential indicator for CML clinical phases