The use of soybean in human and animal nutrition is limited because of high content of bioactive compounds: enzyme inhibitors, polyphenols, goitrogens, phytates, saponins, sugars, and agglutinins. The damage of intestinal mucosa structure was previously observed in animals fed soybean supplemented diets. Hence, the objectives of the presented study were to compare intensity of epithelium remodeling processes in different intestinal segments, and to evaluate the influence of the 1% of soybean dietary supplementation on the processes in intestinal mucosa. The experiment was performed on 30 Wistar rats fed AIN-93 based diets. Animals were divided randomly into three groups: control (CTRL), with 1% of raw soybean (RS) and with 1% of soaked and boiled soybean (BS). The samples of: duodenum (DUO), proximal jejunum (PROX), mid-jejunum (MID), distal-jejunum (DIST) and ileum (ILE) were collected. The following processes in these samples were evaluated: mitosis (Ki-67), apoptosis (Cpp32), autophagy (MAP I LC3) and DNA damage (p53). Present data show that modification of soybean by soaking and subsequent boiling markedly influences the enterocyte turnover in the small intestine mucosa. Increased mitotic ratio in the intestine of rats fed with boiled soybean masks the negative effects of soybean on the small intestine structure.