Abstract The effects of silkworm pupa protein hydrolysates (SPPHs) on the apoptosis of MGC-803 gastric cancer cells were investigated in this study. The role of mitochondrial-dependent apoptosis in SPPHs-dependent inhibition of MGC-803 cell viability was also explored. SPPHs were found to induce apoptosis in MGC-803 cells with an IC50 of 0.30 mg/ml. A series of changes in cellular organelle structural were observed during MGC-803 cell apoptosis that included mitochondrial swelling, vacuolation and rupture. These changes may ultimately impact on metabolic energy supply in MGC-803 cells. The expression of the pro- and anti-apoptotic proteins Bcl-2 and Bax, and the activation of cytochrome c (Cyt C), Caspase-3 and Caspase-9 were altered following induction of apoptosis by SPPHs in MGC-803 cells. Moreover, the increase in the ratio of Bax to Bcl-2 expression is known to play an important role in the activation of the mitochondrial-dependent apoptotic pathway.