Gastrointestinal disorders are still a main world public health problem. Scientific progress shows that and inadequate balance in intestinal microbiota (IM) plays a crucial role in its pathogenesis. Evidence indicates that one way to modulate the IM is through the use of prebiotics. These oligosaccharides stimulate the growth of benefic bacteria and increase the resistance to invading pathogens. Research using animals show that the consumption of prebiotics could be implicated in prevention and treatment of diarrhea. Studies in healthy infants also indicate that the consumption of prebiotic mixtures (galactooligosaccharides/fructooligosaccharides, inulin/galactooligosaccharides) decreases the incidence of fever, infections and pathogens. These results represent a great potential for functional foods that contain prebiotics, mainly the infant formulas. However, results of other clinical studies for prebiotics effects on diarrhea are not conclusive. Specially those studies that include patients with an altered IM (like the elderly), patients with chronic intestinal inflammation and with diarrhea associated to antibiotic treatments. There is a need for more biochemical and microbiological studies in humans at different ages and intestinal health conditions, in order to determine when prebiotics may effectively function on infections.