In this study, the effects of processed small black soybeans on the intestinal morphological characteristics of rats were examined. Adult male rats were fed diets containing raw, cooked, or acidified small black soybean powders for 4 weeks. The total short chain fatty acid (SCFA) level was significantly higher in the acidified small black soybean supplemented group than in the raw and cooked soybean diet groups. The major SCFAs found in the experimental groups were acetate, followed by propionate and butyrate. The duodenal villus height and colonic mucosal thickness were also significantly higher in the acidified small black soybean supplemented group than in the raw and cooked soybean diet groups. The acidified small black soybean supplemented group showed the densest colonic mucosa by staining with alcian blue (AB), as compared to the raw and cooked soybean diet groups. The acidified small black soybean supplemented group exhibited strongly stained $CD4^+$ in the mucosal lamina propria, while cooked and acidified diet groups were more strongly stained $CD8^+$ in the submucosal lamina propria than the raw diet group. These results suggest that acidified small black soybeans may help improve intestinal function.