Background: There are several reports indicating that the isoflavone genistein may augment the integrity of the intestinal epithelial barrier as well inhibit bacterial internalization by cultured enterocytes. We speculated that oral genistein might enhance the integrity of the intestinal epithelial barrier as monitored by the extraintestinal dissemination of intestinal bacteria. Methods: Mice were treated with oral antibiotics to induce cecal bacterial overgrowth accompanied by bacterial translocation of antibiotic-resistant enterobacteria, especially Escherichia coli. These mice were divided into separate groups that included chow-fed mice orally inoculated either with saline, vehicle, or genistein, and mice fed isoflavone-free diet and orally inoculated with either saline, vehicle, or genistein. Intestinal bacterial overgrowth was monitored by quantitative culture of excised ceca and bacterial translocation was monitored by quantitative culture of draining mesenteric lymph nodes. Results: Mice fed the isoflavone-free diet had decreased populations of cecal bacteria compared with chow-fed mice, and bacterial translocation was reduced in chow-fed mice compared with mice fed isoflavone-free diet. However, bacterial translocation was similar in mice given oral genistein compared with appropriate control mice. Conclusions: Oral genistein had no noticeable effect on bacterial translocation in this model. However, the isoflavone-free diet had an antibacterial effect on cecal flora, and the isoflavone-free diet was associated with decreased numbers of cecal bacteria and decreased incidence of bacterial translocation.