The production of bacteriocins is widespread among all bacteria. Their role in the intestinal tract of humans and animals however has been less investigated than in food, mainly because of difficulties associated with the demonstration of their health-contributing effects. The effects of bacteriocins produced by established or potential probiotics against gastrointestinal pathogenic bacteria such as Staphylococcus aureus, Clostridium difficile, Helicobacter pylori, virulent strains of Enterococcus, Campylobacter, Salmonella, Escherichia coli and Listeria monocytogenes have been documented in vitro as well as in a few in vivo studies. Bacteriocins can also contribute to the inhibition of adhesion of intestinal pathogens to the intestinal mucosa by biochemical hindrance. Although there are speculations about the possible direct effects of bacteriocins on the host organism as signalling molecules, there is no clear evidence for that. Despite most bacteriocins are degraded in the stomach and small intestines, some in vivo studies indicated the positive effects of feeding purified bacteriocins (nisin, pediocin PA-1, enterocins) to the animals, such as reduction of pathogens (Salmonella, Campylobacter, Staphylococcus aureus). New possibilities such as the structural analysis (DC spectroscopy, nuclear magnetic resonance), construction of recombinant probiotics with heterologous bacteriocin genes, protein-engineering used to synthesize modified bacteriocins with improved properties, and increasing number of the whole genomes sequences of probiotic bacteria will enable to better identify and understand the relations between structure and function of bacteriocins. We may expect that this will enable the development of future applications of bacteriocins also for the treatment of GI bacterial infections.