To evaluate the probiotic potential of Bacillus polyfermenticus CJ6 isolated from meju, a Korean traditional soybean fermentation starter, its functionality and safety were investigated. B. polyfermenticus CJ6 was sensitive to all antibiotics listed by the European Food Safety Authority. The strain was also non-hemolytic, carried no emetic toxin or enterotoxin genes, and produced no enterotoxins. The resistance of B. polyfermenticus CJ6 vegetative cells and spores to simulated gastrointestinal conditions was high (60-100% survival rate). B. polyfermenticus CJ6 produced high amounts (0.36 g as a purified lyophilized form) of γ-polyglutamic acid (PGA). We speculate that the improved cell viability and the production of γ-PGA have a significant correlation. Adhesion of the strain to Caco-2 and HT-29 cells was weaker than that of the reference strain (Lb. rhamnosus GG), but it was comparable to or stronger than those of reported Bacillus spp. When B. polyfermenticus CJ6 spores were given orally to mice, the number of cells excreted in the feces was 4-fold higher than the original inocula. This suggests the inoculated spores propagated within the intestinal tract of the mice. This idea was confirmed by field emission scanning electron microscopy, which revealed directly that B. polyfermenticus CJ6 cells germinated and adhered within the gastrointestinal tract of mice. Taken together, these findings suggest that B. polyfermenticus CJ6 has probiotic potential for both human consumption and use in animal feeds.