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Salmonellae are among the most widespread sources of foodborne infections and Salmonella Typhimurium, in particular, is correlated with human disease caused by the consumption of contaminated pork. Intraepithelial lymphocytes (IEL) have early contact with intestinal antigens and play an important role in the detection of pathogenic bacteria. The objective of this study was to determine whether a presumed probiotic Enterococcus faecium strain could improve histomorphological and immune system-related parameters of gut function after a Salmonella challenge in weaned pigs. In particular the morphological parameters villus length and width, crypt depth and width as well as the actual enlargement of the intestinal epithelial surface were calculated and the number of IEL was evaluated in sections of the porcine gut. Weaned piglets were challenged with Salmonella enterica serovar Typhimurium DT 104, and half of them also received Enterococcus faecium NCIMB 10415 in the diet. Animals were sacrificed at days post infection (DPI) 2 and 28. The effect of the factors "time post-infection/age" and "probiotic treatment" on jejunal morphology and IEL numbers and distribution was evaluated by light microscopy. The time post-infection had significant effects in both feeding groups. Animals sacrificed at DPI 28 had longer and wider villi, deeper and wider crypts, a higher villus enlargement factor, a higher ratio between villus and crypt enlargement factors as well as more IEL. Probiotic treatment resulted in longer villi, a higher ratio of villus surface/crypt circumference enlargement factors and significantly more IEL. The larger total number of IEL displayed by the probiotic group resulted from significantly higher numbers of IEL at the nuclear and apical levels of the intraepithelial compartment but not from the number of IEL situated at the basement membrane. The probiotic effects were only measurable 28 DPI. It is proposed that Enterococcus faecium NCIMB 10415 exerts an immune modulatory effect by increasing the numbers of intraepithelial lymphocytes.