AIM: To isolate and identify the soybean conglycinin peptides that selectively stimulates the growth of bifidobacteria in vitro, and to investigate the effect of soybean conglycinin peptides on intestinal ecosystem in vivo.METHODS: Soybean conglycinin was purified from soybean seeds by gel filtration (Sepharose-CL-6B). These proteins were submitted to hydrolysis by pepsin. Several growth-stimulating peptides for bifidobacteria were isolated chromatographically from pepsin hydrolysis of soybean conglycinin and identified by means of matrixassisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS). Parallel to in vitro study,in vivo experiments with soybean conglycinin peptides were performed in mice. Ninety male KM mice were randomly assigned into five groups of 16 mice each, and each group was administered for 21d intragastrically with physiological saline (control), conglycinin, pepsin-treated conglycinin (PTC), the most active fraction which isolated from pepsin-treated conglycinin (P2-PTC) and HCl-full hydrolysis of conglycinin (HCl-FHC), respectively. Intestinal microfiora were evaluated by standard microbiologic methods and biochemical assays of cecal content samples after treatment.RESULTS: The results showed that the peptides which were isolated from soybean conglycinin could stimulate the growth of bifidobacteria in vitro, and the molecular mass of purified peptides with MALDI-TOF-MS ranged from 693.32 to 1829.55. Compared with control group,in vivo experiments showed that P2-PTC group decreased cecal pH (7.08±0.08 vs7.21±0.09, P＜0.05) and enterococcicounts (5.38±0.26 log10CFU/g vs 5.78±0.19 log10CFU/g, P＜0.05),significantly increased sIgA level (172.08±35.40 ng/g vs 118.27±33.93 ng/g, P＜0.01) and β-galactosidase activity (1.28±0.23 U/g vs 1.82±0.58 U/g, P＜0.05).CONCLUSION: The results have shown that conglycinin is good source for enzyme-mediated production of peptides which stimulate the growth of bifidobacteria.These peptides are inactive within the sequence of the parent protein but can be released during enzymatic hydrolysis, and in vivo experiments demonstrate that conglycinin peptides may be beneficial for improving gastrointestinal health.