The microbiota that colonizes the gastrointestinal tract confers health benefits to the host by contributing to dietary digestion, regulating immunity and preventing pathogen colonization and invasion. Lactic acid bacteria (e.g. Lactobacillus) and Bifidobacterium constitute the main groups of probiotics commercialized for human consumption. The prevention and treatment of gastrointestinal infections continues to be complex due to the expansion of antibiotic resistances. The possible uses of probiotics and derived products as therapeutic or preventive drugs against gastrointestinal infections have been intensively investigated, as reflected in a large number of published patents. The possible mechanisms of action of probiotics against gastrointestinal pathogens addressed in diverse patent applications include: (i) modification of the environmental conditions, (ii) competition for nutrients and adhesion sites, (iii) production of antimicrobial compounds, (iv) modulation of the immune and nonimmune defense mechanisms of the host, and (v) regulation of the intestinal neuromuscular function. The molecules responsible for the antimicrobial effects of probiotics include cell-wall fractions, surface proteins, nucleic acids, organic and short-chain fatty acids, antimicrobial proteins and other less-well identified soluble factors. The effectiveness of probiotics is supported by human clinical trials on treatment of acute diarrhea, prevention of antibiotic associated-diarrhea and as adjuvant therapy with antibiotics in eradication of Helicobacter pylori infection. Probiotics and their bioactive compounds constitute attractive alternative or adjuvant drugs as they can reduce the use of antibiotics and improve conventional pharmacological therapies. The advances in the knowledge of novel bioactive molecules and the intricate host-microbe interactions within the intestine and extra-intestinal sites will result in the future development of a new generation probiotic-based products targeting a broader range of pathologies.