The effects of non-fermented soybean milk (NFSM) and fermented soybean milk (FSM) intake on the faecal microbiota and metabolic activities in 10 healthy volunteers were investigated. Soybean oligosaccharides, raffinose and stachyose were utilized by bifidobacteria except for Bifidobacterium bifidum, but most strains of Escherichia coli and Clostridium perfringens could not use them. During the dietary administration of FSM, the number of bifidobacteria and lactobacilli in the faeces increased (p < 0.05), and clostridia decreased (p < 0.05). Moreover, the concentrations of faecal sulphide were decreased (p < 0.01) in the intake of FSM. During the dietary administration of NFSM, the number of bifidobacteria tended to increase. These results indicate that the consumption of soybean milk, especially FSM, is related to improvement of the intestinal environment.