This study was to investigate the effects of DAPT (N-[N-(3,5-difluorophenacetyl-L:-alanyl)]-S-phenylglycine-butyl ester) on cell cycle, apoptosis, differentiation and expansion of hematopoietic stem cells (HSC) of mouse and to elucidate the possible mechanisms. The mRNA expressions of cell cycle-related genes p18, p21, p27, CDK1, CDK2, CDK4, CDK6, and apoptosis-related genes Bcl-2, Bcl-xl, mcl-1, Bax, Bim, p53, Puma were measured by real-time PCR. The cell cycle and apoptosis of Lin(-)c-kit(+)Sca-1(+) marked cells and CD34(-)Lin(-)c-kit(+)Sca-1(+) marked cells in bone marrow cells were detected by flow cytometry. The differentiation level of HSC was determined by single cell culture. The expansion of HSC were measured with long-term culture. The results indicated that the mRNA expression of the cell cycle related-genes CDK1, CDK2, CDK4, CDK6, p27 in Lin(-) c-kit(+)Sca-1(+) marked cells increased (P < 0.05), the expression of p18, p21 decreased (P < 0.05), the expression of the apoptosis related-genes Bcl-2, Bcl-xl, Bax, p53, Puma in Lin(-) c-kit(+)Sca-1(+) marked cells increased (P < 0.05), the expression of Bim decreased (P < 0.05), the expression of Mcl-1 had not changed (P > 0.05) after treatment with DAPT 1 µmol/L for 5 d. The changes of cell cycle of Lin(-)c-kit(+)Sca-1(+) marked cells in bone marrow had no statistical significance after treatment with DAPT 1 µmol/L for 5 d, CD34(-)Lin(-)c-kit(+)Sca-1(+) marked cells in bone marrow at G(0) phase decreased and at G(1) phase increased after treatment with DAPT 1 µmol/L for 5 d (P < 0.05); the apoptotic fractions of Lin(-) c-kit(+) Sca-1(+) marked cells and CD34(-)Lin(-)c-kit(+)Sca-1(+) marked cells in bone marrow increased after treatment with DAPT 1 µmol/L for 5 d (P < 0.05). The changes of colony number, average number of cells in wells and their differentiation had no statistical significance (P > 0.05) after treatment with DAPT 1 µmol/L for 10 d. Expansion of HSC in bone marrow of mouse decreased after treatment with DAPT 1 µmol/L for 3 d. It is concluded that DAPT not only enhances the exhaustion of CD34(-)Lin(-)c-kit(+)Sca-1(+) marked cells in bone marrow cells of mouse, but also enhances the apoptosis of Lin(-)c-kit(+)Sca-1(+) marked cells and CD34(-)Lin(-)c-kit(+)Sca-1(+) marked cells in bone marrow cells of mouse. DAPT also reduces the expansion of HSC. However, the changes of survival and differentiation of single CD34(-)Lin(-)c-kit(+)Sca-1(+) marked cells in mouse bone marrow cells have no statistical significance.