Abstract: The in vitro colon cancer cells inhibitory effects of glass and stainless steel vessels fermented Shuidouchi were determined in this study. Two kinds of Shuidouchi ethanol extracts contained more genistein and raffinose than raw soybean ethanol extract ( RS) , genistein and raffinose contents of glass vessel fermented Shuidouchi ethanol extract ( GVFS) were higher than stainless steel vessels fermented Shuidouchi ethanol extract ( SSVFS) .GVFS had the strongest colon cancer cells inhibitory effects, and the colon cancer cells inhibitory effects of SSVFS were higher than RS by the experiments of in vitro cultured HT-29 and HCT-116 colon cancer cells. The results of further RT-PCR experiment also showed that GVFS, SSVFS and RS could raise Bax, Caspase-3, Caspase-8, Caspase-9 mRNA expressions of colon cancer, and reduce Bcl-2, Bcl-x L expressions, the effects of GVFS were stronger than SSVFS and RS. From the results, GVFS contained highest genistein and raffinose contents, and GVFS had highest cancer cells inhibitory effects and apoptosis inducing effects, glass vessel could be used for high physiological activities Shuidouchi fermentation.