Background:In recent years, Flexible Fiberoptic Bronchoscopy (FFB) has been applied for diagnostic and some therapeutic purposes. During FFB and even in the presence of supplemental oxygen, hypoventilation leading to hypoxia and desaturation may occur; this is aggravated by the use of suction. Arterial oxygen saturation is usually monitored with pulse oximetry (Spo 2 ) during FFB; End-Tidal Pco 2 (ET-Pco 2 ) monitoring is not routinely used. Methods: Two-hundred patients were studied between May 1998 till April 2003, at the divisions of chest surgery and Pulmonology at King Hussein Medical Center, (KHMC). Their ages 53±19 years (mean±SD), underwent FFB and received supplemental oxygen during various stages of FFB: 1-before and during installation of lidocaine on the vocal cords, 2-during passage of instrument into the trachea, RMB, IMB, 3-during bronchoalveolar lavage, bronchial biopsy, Trans Bronchial Biopsy (TBB), and 4-at the final stages of FFB. ET-Pco 2 changes were studied with a capnograph and Spo 2 using a pulse oximeter simultaneously and the results were recorded. Results: Mean ET-Pco 2 significantly decreased from 28.7±4.5 mmHg before FFB to 28±5.7 mmHg, 27.9±5.5 mmHg, 27.5±5.6 mmHg, 27.1±4.5 mmHg, 27.9±5.3 mmHg during bronchoscopy of the Right Main Bronchus (RMB), Left Main Bronchus (LMB), bronchial washing, bronchial biopsy and Trans Bronchial Biopsy (TBB), and at the termination of FFB, respectively (p<0.05). In 118 patients (59%), the decrease of ET-Pco 2 was equal to or greater than 4 mmHg; in 105 patients (52.5%) the amount of decrease in Spo 2 was = 5% and in 32 patients (16%), Spo 2 decreased = 10%. No correlation was found between decreasing ET-Pco 2 and Spo 2 during the procedure. Conclusion: ET-Pco 2 and Spo 2 decreased during bronchoscopy. We also speculate that this reflects airway obstruction by the instrument. Further studies and more experimental analysis in this field is recommended.