INTRODUCTION: Colonization of the lower respiratory tract is an independent risk factor for ventilator-associated pneumonia. Little is known about the frequency of viral colonization on intubation and during mechanical ventilation. METHODS: Overall, 65 eligible intubated patients with no initial signs of pulmonary infection were studied over a period of up to 7 days. Tracheobronchial aspirates were taken: (i) within 48 h after intubation; and (ii) when clinical signs of nosocomial tracheobronchitis were present, before extubation, or after 7 days. Presence of respiratory viruses was investigated using quantitative polymerase chain reaction. RESULTS: Patients were 67 +/- 11 years old and had been in hospital for 5.1 +/- 8.4 days when intubated (major cause for intubation: cardio-pulmonary resuscitation 25/65, 38%). The average Acute Physiology and Chronic Evaluation II score was 27.3 +/- 4.9. Microbiology detected Candida spp. (17/65; 26%) and Staphylococcus aureus (methicillin sensitive: 11/65; 17%; methicillin resistant: 3/65; 5%) and only few respiratory viruses (4/65, 6%). Thirty-eight percent of the samples (25/65) were sterile. At the given endpoints, 27/65 (42%) patients were available for follow-up and only one aspirate became positive for respiratory syncytial virus (RSV). CONCLUSIONS: After endotracheal intubation, fungi, but not viruses were most frequently isolated. Only one patient acquired RSV, therefore colonization with respiratory viruses does not seem to play a major role early after intubation.