Objective To explore cell cycle distributions and expressions of CD34 and Ki67, and cell proliferation-related proteins in bone marrow mononuclear cells(BMMNCs) among myelodysplastic syndromes(MDS), aplastic anemia(AA), and acute leukemia(AL) patients. Methods Bone marrow aspirates were collected from 68 patients between June 2009 and June 2010 at the Department of Hematology, Provincial Hospital affiliated to Shandong University.The cases consisted of 30 MDS (18 refractory anemia and 12 refractory anemia with excess blasts), 22 AA (7 severe and 15 non-severe cases), and 18 AL (12 acute myeloid leukemia and 4 acute lymphoblastic leukemia). 18 healthy individuals without any hematological problems were used as normal controls. Propidium iodide and immunofluorescent double staining through flow cytometry were applied to explore the cell cycle distributions and expression of CD34 and Ki67. Results Compared with the control group, the percentages of G0/G1 phase of the cell cycle, haemopoietic stem/progenitor cells CD34+ cells, Ki67+ cells, CD34+Ki67+ cells, Ki67+ cells in CD34+ cells, and CD34+ cells in Ki67+ cells of BMMNCs were all significantly increased in the MDS and AL group(P<0.05), whereas the percentages of S and S+G2/M phases of the cell cycle were both significantly decreased(P<0.05). In addition, the proportion of G2/M phase of the cell cycle was lower in the AL group than the control group(P<0.05). The ratios of G0/G1 phase, CD34+ cells, Ki67+ cells, CD34+Ki67+ cells, Ki67+ cells in CD34+ cells, and CD34+ cells in Ki67+ cells were significantly higher in RAEB(refractory anemia with excess blasts) compared to RA(refractory anemia) and in AL compared to RAEB (P<0.05), accompanied by lower ratios of S and S+G2/M phases (P<0.05). There were no significant differences in the ratios of G0/G1, S, G2/M, and S+G2/M phases of BMMNCs between the AA and the control group (P>0.05), whereas the proportions of CD34+, CD34+Ki67+, Ki67+ cells in CD34+ and CD34+ cells in Ki67+ cells were all significantly lowered in the AA group (P<0.05). The percentages of G0/G1 phase, CD34+ cells, Ki67+ cells, CD34+Ki67+ cells, Ki67+ cells in CD34+ cells, and CD34+ cells in Ki67+ cells were more significantly increased in the RA group than in the AA group (P<0.05), whereas the ratios of S and S+G2/M phases were both significantly decreased (P<0.05). Conclusion This study suggests that AA is different from MDS and AL. There is similar pathogenesis for MDS and AL. Analyses of the cell cycle and cell proliferation in bone marrow mononuclear cells are reliable approaches for the diagnosis and differential diagnosis of RA and AA.