Probiotics are nonpathogenic microorganisms mostly of human origin which, when administered in adequate amounts, confer a health benefit on the host and enable to prevent or improve some diseases. Probiotics may be a natural temporary constituent of the resident intestinal microflora, but their concentration is not sufficient for therapeutic purposes. The microbiota, the intestinal epithelium, and the mucosal immune system constitute the gastrointestinal ecosystem. All three components are essential for complete functional and developmental maturity of the system. The viability of intestinal microflora (including probiotic strains) requires the availability of nutritional substrates (prebiotics), i.e. various types of fiber and oligosaccharides. Prebiotics are cleaved by microbial enzymes to numerous substances (short-chain fatty acids, aminoacids, polyamines, growth factors, vitamins and antioxidants) indispensable for metabolic and functional activities of the intestinal mucosa. The principal probiotics in use include lactobacilli, bifidobacteria, some nonpathogenic strains of Escherichia coli, and Saccharomyces boulardii. These microbiota display favourable effects which qualify them for therapeutic use. For this purpose, probiotics have to fulfill a series of requirements verifying their efficacy and safety. Experimental and clinical studies examine the prerequisites for the administration of probiotics in digestive diseases, allergic and atopic affections, as well as in some extraintestinal conditions. Future goals of probiotic application include genomic analysis, controlled postnatal colonisation of the digestive tract, the use of probiotics as carriers of peroral vaccines, and recombinant probiotics with in-situ production and targeted application of therapeutic molecules.