Cathepsin B, a lysosomal cystein protease that plays an important role in the degradation of intracellular proteins in lysosomes, is detected in a wide variety of cells including bovine oocytes and embryos. Although the mode of action of cathepsin B is not fully understood, a strong relationship was observed between cathepsin B and apoptosis in many types of cells. Cathepsin B was found to induce the apoptotic pathway through activating initiator caspases rather than executioner caspases. Thus, the aim of this study was evaluated the effect of capthesin B inhibitor, E-64, on blastocyst developmental competence and subsequent preimplantation quality of the IVF and SCNT bovine embryos. After IVF and SCNT procedures, presumptive bovine embryos were cultured in CR1aa medium supplemented with E-64 for 24 h. Then, samples were additionally cultured in CR1aa medium without E-64 for 5 days. In our results, the frequency of blastocyst formation was higher when treated with E-64 compared with the control group (p<0.05). Furthermore, the blastocyst cell number was enhanced and apoptosis reduced (TUNELpositive nuclei number) by E-64 treatment in both IVF and SCNT bovine embryos (p<0.05). In the real-time quantitative RT-PCR, the expression of anti-apoptotic Bcl-xL gene was shown to be increased in the blastocyst stage, whereas expression of proapoptotic Bax was decreased. In conclusion, our results indicate that E-64 improves the developmental competence and embryonic qualities of bovine IVF and SCNT embryos by modulating cathepsin B induced apoptosis during the preimplantation stage.