Infection of the lower airways is a major problem in ventilated patients and contributes substantially to morbidity and mortality in the intensive care unit. The selective decontamination of the digestive tract and its effect on the reduction of the gram-negative colonisation rate in patients has been studied widely. However, the findings are inconsistent. Most studies describe an increase in resistant gram-negative bacterial strains and/or an increase in the occurrence of gram-positive strains following selective decontamination of the digestive tract. In light of the unresolved questions concerning the efficacy of selective decontamination of the digestive tract, it would seem that the resultant effect of this treatment on the bacterial flora should be an important consideration when assessing the value of such treatment. To date, none of the studies available for examination have been designed to adequately assess the effect of selective decontamination of the digestive tract on the bacterial flora.