Enteral tube feeding is common in both the hospital and community environment; however, patients can suffer alterations in faecal output that can have serious clinical sequelae. Problems associated with accurate characterisation of faecal output and definition of diarrhoea impede the comparison of research studies and prevent standardised assessment of therapeutic interventions in clinical practice. The colonic microflora may protect the patient against diarrhoea by preventing enteropathogenic infection and by producing SCFA that stimulate colonic water absorption. However, studies in healthy volunteers suggest that the composition of the enteral formula may have a negative impact on the microflora and SCFA concentrations. The addition of fructo-oligosaccharides to the enteral formula may partially prevent negative alterations to the microflora, although conclusive data from studies in patients are not yet available. Modification of the microflora with probiotics and prebiotics may hold potential in prophylaxis against diarrhoea during enteral tube feeding.