Dietary probiotics should reach the intestine viable and in high numbers; therefore, they should tolerate the stress associated to the gastro-intestinal (GI) environment. Indeed, all along the different GI sections, probiotics are challenged by several sources of stress, including low pH, bile and digestive enzymes. Bacterial cells are equipped with various defense mechanisms to allow survival in hostile environments. The food matrix used to deliver beneficial bacteria may contribute to their probiotic action, e.g. by enhancing survival to stress and gut colonization. In this study, the survival of the lactic acid bacterium Lactobacillus plantarum WCFS1, a model probiotic strain, was examined in a human oro-gastric-intestinal (OGI) in vitro system, using different carrier matrices to compare protective and buffering properties. Higher survival was observed in complex and/or nutrient-rich matrices, and when potential prebiotics were added. The molecular response of L. plantarum to the OGI transit was analyzed by studying the transcriptional levels of genes involved in stress response and probiosis. The OGI steps of higher mortality corresponded to greater induction of stress genes, thus implying their involvement in adaptation to the gut environment. Plantaricins were significantly upregulated all along the different OGI sections; adhesion genes were mainly induced by gastric environment.