In a feeding experiment, the probiotic Bacillus cereus var. Toyoi was fed to sows and piglets in order to test whether it influences the stress response of enterocytes, thereby causing intestinal immune activation, possibly accompanied by an impairment of the epithelial integrity. The impact of B. cereus on the piglets' intestinal enterocytes (EC) and on the communicating intraepithelial lymphocytes (IEL) was investigated during the weaning phase where significant immunological changes might be expected. The expression of the stress-induced MHC class I-related molecule 2 (MIC2) and the UL16 binding protein (ULBP) was measured in jejunal EC and the frequencies of the main present IEL populations in the jejunum were monitored. To find out which of the IEL populations can be activated by the stress-induced molecules the sorted IEL were tested for the expression of the activating natural killer receptor 2D (NKG2D). The piglets fed with B. cereus showed an impaired intestinal barrier function shortly after weaning. However, a significant impact on the expression of stress-induced molecules was not observed. The mRNA expression of NKG2D was confirmed in intraepithelial CD5+ γδ T cells. The ratio of IEL (CD45+) to EC was lower in the B. cereus treated group, which could be explained by lower frequencies of CD8αβ+ T cells in the jejunal epithelium (p ≤ 0.005 for ages 32 and 34). Although a consistently increased expression of stress-induced MHC class I-related molecules was not found, this study suggests a negative impact of B. cereus on the intestinal barrier function and supports immune-modulating properties of the probiotic feed supplement.