We focused on investigation of E. coli infection influence on the turnover and apoptosis of intestinal mucosa. We have verified changes in proliferation and apoptosis in epithelial lining as well as in lamina propria of jejunum and colon of germ-free (GF) piglets as healthy control group and GF piglets in which at 5th day their gut was colonized with E. coli bacteria (ECK group). According to our results we detected significant increase in proliferation of the epithelial cells only in the jejunum of the ECK group, indicating a higher sensitivity to colonization with E. coli. Significant changes in the TUNEL assay and immunohistochemistry of other studied markers (TNF-α, Caspase-3 and HSP-70) were noted only in the lamina propria mucosae of both intestinal segments in the ECK group. In conclusion, we found that the commensal gut microbiota plays a role in regulation of the turnover rate in the epithelial lining, but also in the cells in the lamina propria mucosae in both intestinal segments, and that the host response is dependent on the colonising bacteria.