Germ-free rats were inoculated with microbial flora from feces of conventionally reared rats and the mucosal structure was quantitatively observed at different time intervals after the inoculation and at different regions of the small intestine. In the ileum, desquamation figures were frequently seen on the villus tip, and several parameters of the mucosal elements, i.e., villus and crypt lengths, mitotic figures, goblet cells and thickness of lamina propria were significantly increased after the inoculation. On the other hand, in the duodenum and jejunum, such parameters except for the lamina propria showed no remarkable change during the course of the experiment, though the villus/crypt ratio increased temporarily at half a day after the inoculation. These regional differences of the mucosal response to the inoculation may be due to the different populations of microbial flora which settled in each region of the small intestine.