Background: The aim of this study was to investigate systemic changes that can occur in critically ill patients shortly after flexible bronchoscopy and to determine plasma cytokine levels during this period as an expression of a systemic inflammatory response. Methods: A prospective and observational study was performed in a 17-bed medical-surgical intensive care unit. Patients with indications for bronchoscopic bronchoalveolar lavage (BAL) were prospectively and consecutively included during a time of study of 27 months, from October 2006 to December 2008. Heart rate, blood pressure, and temperature were recorded. Microbiological analysis of respiratory samples was carried out. The levels of interleukin 6 (IL-6), interleukin 8 (IL-8), tumor necrosis factor alpha, granulocyte colony-stimulating factor, and granulocyte-macrophage colony-stimulating factor were determined 4 hours before flexible bronchoscopy, immediately after, 4 hours after, and 24 hours after the procedure; cytokine levels in BAL were also measured. Results: A total of 59 patients undergoing flexible bronchoscopy with BAL were included. A statistically significant, yet transient, decrease in blood pressure was observed 4 hours after the procedure, from 90.7 +/- 13.9 mm Hg to 80.7 +/- 14 mm Hg, which was correlated with a significant IL-6 concentration increase from 127 +/- 164.5 pg/mL to 196.4 +/- 238.2 pg/mL at the same time point. Conclusions: BAL in mechanically ventilated patients causes a statistically significant blood pressure decrease 4 hours after the procedure in a high percentage of cases that correlates with a systemic inflammatory response resulting from increased IL-6 plasma levels.