Most cases of antibiotic-associated diarrhoea (AAD) are directly or indirectly due to the alteration of gut microflora by antibiotics. 'Functional' diarrhoea, usually limited to a mild and brief change in stool frequency, is considered as the most frequent pattern of AAD. Reduced carbohydrate fermentation and impaired metabolism of bile acids have been claimed as the potential causes of this transient digestive discomfort but a critical analysis of the data supporting these theories is necessary. Alternatively, changes in the gut flora ecosystem allow pathogens to proliferate. Clostridium difficile is responsible for approximately 10% of cases of AAD and almost all cases of antibiotic-associated pseudomembranous colitis. The level of evidence which supports the potential responsibility of other candidate pathogens (Klebsiella oxytoca, enterotoxin-producing Clostridium perfringens and Staphylococcus aureus, Candida) needs to be appreciated according to the updated postulates of causality relationships between a bacterium and a disease.