The source of ventilator-associated pneumonia (gastric or oropharyngeal flora) remains controversial. We investigated the source of bacterial colonisation of the ventilated lung in 100 consecutive intensive-care patients. Gram-negative bacilli were isolated from the lower respiratory tract in 19 patients. Bacteria isolated from the stomach contents either previously or at the same time were identical to lower respiratory isolates in 11 patients. No gram-negative oropharyngeal isolate was identical to a lower respiratory tract isolate. Gastric bacterial overgrowth with gram-negative bacilli was associated with the presence of bilirubin in the stomach contents. Detectable bilirubin was also associated with subsequent acquisition of gram-negative bacilli in the lower respiratory tract. Only 5 gastric aspirate specimens with pH < 3.5 contained gram-negative bacilli. These results establish a relation between duodenal reflux and subsequent bacterial colonisation of the lower respiratory tract. Restoration of normal gastroduodenal motility might help prevent pneumonia in intensive-care patients.