The effects of Lactobacillus collinoides JCM1123T on plasma cholesterol levels, isoflavonoids in the caecum and faecal flora were assessed in adult mice. L. collinoides JCM1123T altered the equol production status in in vitro incubation of daidzein with faecal flora of mice. In in vivo investigation, mice were fed an AIN-93M purified diet for 13 days, and then randomly divided into two groups of seven animals each. All mice were fed an AIN-93M diet for 6 days; then the diet was replaced with a 0.05% daidzein diet, the mice received a 0.05% daidzein diet for 4 days. Two groups of mice were administered either L. collinoides JCM1123T (the experimental group) or a physiological saline solution (the control group) daily for 10 days and dissection was performed on the following day. The total plasma cholesterol concentration was significantly higher in the control group than in the experimental group. The amount of daidzein present in the caecum was significantly higher in the control group than in the experimental group. Significantly higher numbers of lactobacilli were observed in the experimental group than in the control group. Our data suggest that the administration of L. collinoides is likely to influence the metabolism of isoflavonoids and endogenous cholesterol via changes in the gastrointestinal environment.