Background Recent studies have shown that interleukin-3 receptor a (CD123) is highly expressed on leukemia stemcells of patients with acute myeloid leukemia, and is correlated with tumor load and poor prognosis. The expression ofCD123 may also be high in patients with myelodysplastic syndrome (MDS). In this study, the expression and clinicalsignificance of CD123 and granulocyte colony stimulating factor (G-CSF) receptor (CD114) on the bone marrow cells ofpatients with MDS were investigated to explore the molecular marker of the malignant clone of MDS.Methods Forty-two patients with MDS, who were diagnosed in the Hematological Department of General Hospital ofTianjin Medical University from 2008 to 2009, and twelve normal controls were enrolled in this study. Fluorescenceactiviated cell sorter (FACS) was used to measure the expression of CD123 on CD34CD38cells and CD114 on CD34cells of the bone marrow of these patients and controls and the clinical significance was analyzed. The expression ofCD114 on CD123CD34CD38cells was further measured to explore the molecular marker of the malignant clone inMDS.Results MDS patients displayed significantly higher proportion of CD34CD38/CD34((14.03±5.27)%) than normalcontrols ((7.70±4.36)%, P<0.05). The expression rate of CD123CD34CD38/CD34CD38was significantly higher inMDS patients ((48.39±28.15)%) than that in normal controls ((8.75±11.71)%, P<0.01). The expression level of CD123was significantly correlated with the proportion of bone marrow blasts (r=0.457, P <0.05). The expression rate ofCD114CD34/CD34was lower in MDS patients ((33.05±21.71)%) than that in normal controls ((38.99±19.07)%) butwas not statistically significant (P>0.05). The expression of CD114 on CD123CD34CD38cells ((34.82±29.58)%) wassignificantly lower than that on CD123CD34CD38cells ((53.48±27.41)%) of MDS patients (P<0.05).Conclusions MDS patients displayed higher proportion of CD34CD38/CD34than normal controls. CD123 washighly expressed in the bone marrow of the patients with MDS, significantly correlated with the proportion of bone marrowblasts, and thus might be the marker of MDS malignant clone. CD123CD34CD38cells exhibited lower expression ofG-CSF receptors, which might partly explain why MDS clone responds worse to G-CSF in vitro and in vivo.