Diarrhoea is a common and serious complication of enteral tube feeding. Its pathogenesis involves antibiotic prescription, enteropathogenic colonization and abnormal colonic responses, all of which involve an interaction with the colonic microbiota. Alterations in the colonic microbiota have been identified in patients receiving enteral tube feeding and these changes may be associated with the incidence of diarrhoea. Preventing negative alterations in the colonic microbiota has therefore been investigated as a method of reducing the incidence of diarrhoea. Probiotics and prebiotics may be effective because of their suppression of enteropathogenic colonization, stimulation of immune function and modulation of colonic metabolism. Randomized controlled trials of probiotics have produced contrasting results, although Saccharomyces boulardii has been shown to reduce the incidence of diarrhoea in patients in the intensive care unit receiving enteral tube feeding. Prebiotic fructo-oligosaccharides have been shown to increase the concentration of faecal bifidobacteria in healthy subjects consuming enteral formula, although this finding has not yet been confirmed in patients receiving enteral tube feeding. Furthermore, there are no clinical trials investigating the effect of a prebiotic alone on the incidence of diarrhoea. Further trials of the efficacy of probiotics and prebiotics, alone and in combination, in preventing diarrhoea in this patient group are warranted.