In recent years flexible fiberoptic bronchoscopy (FFB) has been applied to children for diagnostic and therapeutic purposes. Sedation during FFB, along with introduction of the bronchoscope into the pediatric airway, may cause hypoventilation, leading to hypoxia and desaturation, even in the presence of oxygen supplementation. Arterial oxygen saturation is usually monitored by pulse oximetry (SpO2) during FFB. End-tidal PCO2 (P(etCO2)) monitoring is not routinely used. Twenty-two pediatric patients (15 days to 18 years old) undergoing FFB and receiving supplemental oxygen were studied prospectively and had continuous P(etCO2) and SpO2 measured before and during the procedure (bronchoscope at the carina or either main bronchus). Mean P(etCO2) (+/- SD) decreased from 33.9 (+/- 6.0) mmHg before to 27.1 (+/- 12.1) mmHg during the procedure (P < 0.024). Concomitantly, mean SpO2 (+/- SD) also decreased from 99.9 (+/- 0.4)% before to 95.7 (+/- 11.1)% during the procedure (P < 0.015). P(etCO2) changes seemed to precede the variations in SpO2, especially in young patients who experienced significant desaturation and decompensation during FFB. We conclude that PetCO2 and SpO2 decrease during FFB in children, even with supplemental oxygen. We speculate that this reflects airway obstruction by the instrument. Further studies are needed to assess the utility of PetCO2 monitoring in pediatric FFB.