Manipulation of the intestinal microbiota with beneficial microorganisms represents a promising alternative and support to the treatment of intestinal inflammation and disorders in intestinal epithelial barrier function. Probiotics can stimulate both the adaptive and innate immune responses. The aim of the study was therefore to clarify the signalling pathways in intestinal epithelial cells triggered by probiotic bacterial strains Lactobacillus gasseri K7 (K7), Lactobacillus fermentum L930BB (L930BB), Bifidobacterium animalis subsp. animalis IM386 (IM386) and Lactobacillus plantarum WCFS1 (WCFS1). The starting point of the research was an in vivo study in which the protective effect of strains L930BB and IM386 was examined in a mouse model with induced colitis. Results of mice colon transcriptome analysis revealed changes in gene expression, involved in activation of anti-apoptotic pathways through phosphatidylinositol 3-kinase (PI3K)/Akt and activation of pathways that lead to regulation of actin cytoskeleton and tight junctions through protein kinase C (PKC). Reorganisation of actin cytoskeleton and decreased apoptosis are both helpful in intestinal epithelial cell monolayer reconstitution. We proved in in vitro experiments that activated signalling pathways are a consequence of signalization through the innate immune receptor Toll-like receptor 2 (TLR2). With the use of flow cytometry we confirmed that probiotic strains and TLR2 ligand are able to reduce cytokine induced cell death. By examining the intestinal epithelial cell line Caco-2 under the confocal microscope, we observed that probiotic strains, in addition to the simulation of inflammatory conditions with H2O2, reduce the internalization of the tight junction protein ZO-1 and thus stabilize intercellular connections. In inflammatory conditions, the addition of probiotic strains also reduced the permeability of the cell monolayer, further proving the protective effect of selected strains and their ability to support the maintenance of the intestinal epithelial barrier.