Probiotics are cultures of beneficial bacteria from the healthy gut microflora that improve the balance of the intestinal milieu by modifying the intestinal microflora and suppressing enhanced inflammatory responses. Probiotics are currently the subject of intense and widespread research as functional foods since they are known to induce health benefits, may be used as pharmaceutical preparations, and have achieved a "generally recognized as safe" (GRAS) status. Lactobacillus strains can also be genetically engineered for use in oral immunotherapeutic applications, such as vaccination and delivery of immunoregulatory substances. In the present review we evaluate the two different approaches to the therapeutic use of probiotics. We also focus on recent findings in the field of molecular biology and genetics of the intestinal immune response related to the microflora and intestinal ecology, in order to understand the mechanisms of action of probiotics and their present indications in gastrointestinal diseases. Finally, with a view to future perspectives we provide some examples of probiotics that are being assessed and have great potential in improving the health of animals and man.