The aim of the study was to determine the effect of Jerusalem artichoke and probiotics on defence activity of intestinal cells of weaning pigs. One hundred eighty piglets (7 weeks old) were fed with basal feed supplemented with Jerusalem artichoke, Lactobacillus reuteri and Pediococcus pentosaceus. After 5 weeks, the piglets were slaughtered and the gastrointestinal contents and intestine samples were taken for analysis. Results demonstrated that in pigs fed basal diet with both probiotics and Jerusalem artichoke (5% of basal diet) (T3 group) had less (P<0.05) faecal Enterobacteriaceae microorganisms and coliforms and had more (P<0,05) faecal Lactobacillus than in pigs from other groups. Increase by 2% of Enterobacteriaceae and E. coli levels were seen only in control piglets (T1 group). E. coli O157 was found at the closing stage in the piglets fed basal diet with only Jerusalem artichoke powder (T2 group), but Salmonella enteritidis - only in T1 group. In jejunum of T2 group piglets, large deterioration of crypts, a moderate inflammation process and plasmocytes were seen, but in jejunum of T3 group piglets - branching of apical surface of villi, moderate degeneration and mitosis of enterocytes were observed. A moderate number of apoptotic cells in T2 group was found mainly in colon inflammation cells and plasmocytes, but for T3 group piglets--both in jejunum enterocytes and migrating cells. Our study indicated that beta-defensin 2 and 3 expression in jejunum and colon segments were incresed in T1 and T2 groups. Findings suggest that feeding with probiotics and Jerusalem artichoke significantly improves the microbial contents, defence and regeneration processes in the intestine of pigs.