Interest in functional foods has increased due to their relationship to diet and health. A healthy nutrition preserves the intestinal ecosystem and enhances health. Probiotic Lactobacillus appears to be highly sensitive to diet, environmental factors, stress, and antibiotics. Functional foods are known to play an important role in the stability of a human intestinal ecosystem. Moreover, dissemination of antibiotic resistances into consumed dairy and meat products could select some bacterial species. However, awareness of the relationship between food and health must be constant through permanent surveillance systems. The European Union guidelines should be imposed for the safe use of functional foods as foods or either as biotherapeutic agents. Functional foods are foods that surpass classic nutritional habits and have usually beneficial action for their host. They are classified into three main classes: probiotics, prebiotics, and symbiotics. The use of genetically modified probiotics could provide further chances for the industrial and pharmaceutical exploitation of probiotic microorganisms. In contrast, prebiotics are not microorganisms but non-digestible components. They stimulate the growth and/or the activity of several bacteria in a beneficial way. Their action contributes to a healthy and balanced intestinal microbiota. Systematic administration of prebiotics decreases blood lipid counts, as well as blood pressure, but increases the synthesis and absorption of foods and maybe has an anticarcinogenic action. They are also used extensively in the food industry. Last but not the least is the class of symbiotics, which combines a mixture of probiotics and prebiotics with both effects.