We studied the interrelations between gastric, pharyngeal, proximal, and distal airway bacterial flora in ventilator-associated pneumonia (VAP) on 36 patients with nosocomial pneumonia acquired during mechanical ventilation (MV) and 27 mechanically ventilated control subjects without pulmonary infection. Gastric, pharyngeal, and endotracheal (EA) sampling for quantitative cultures were performed upon all patients, as well as fiberoptic bronchoscopy with protected specimen brush (PSB) sampling. Mean bacterial and fungi colony counts were significantly increased in pharyngeal, EA, and PSB samples in patients with VAP compared with control subjects. The overall increase in colonization was due to gram-positive cocci in all samples. In addition, gram-negative bacilli and fungi mean counts increased significantly in PSB pneumonia samples versus control samples. However, mean gastric colonization was similar in both patients with VAP and control subjects. In the former group there was an increase in coincident microorganisms isolated from gastric, pharyngeal, and EA samples in relation to PSB samples compared with control samples. Among the different quantitative cultures analyzed, only those obtained from EA significantly correlated with PSB cultures in patients with pneumonia (r = 0.67, p = 0.001). In summary, the present study shows that the coincidence between microorganisms isolated in PSB cultures and those from gastric and oropharynx increase in MV patients with pneumonia, indicating that both reservoirs play a key role in the pathogenesis of pneumonia. Conceivably, preventing both gastric and pharyngeal colonization may reduce the incidence of ventilator-associated pneumonia. From all the noninvasive samples studied only endotracheal aspirate cultures were useful for inferring the etiology of some VAP pneumonias.