This prospective study evaluated the incidence and severity of arterial oxygen desaturation during gastrointestinal endoscopy. Following pulmonary function testing, 115 male patients underwent esophagogastroduodenoscopy (EGD), colonoscopy, or colonoscopy followed by EGD, with continuous recording of arterial oxygen saturation (SaO2). Most patients (80/115, 70%) showed arterial oxygen desaturation (greater than 4% decrease from baseline SaO2); severe arterial oxygen desaturation (SaO2 less than or equal to 85%) reflecting hypoxemia (PaO2 less than or equal to 50 mm Hg) was noted in one-third of patients overall (37/115, 32%). Severe arterial oxygen desaturation occurred in 9/62 EGD patients (15%), 23/46 colonoscopy patients (50%), and 4/7 patients having colonoscopy followed by EGD (57%). Arterial oxygen desaturation occurs frequently during gastrointestinal endoscopy and is often severe. These data support the concept that continuous monitoring of SaO2 should be standard procedure during all gastrointestinal endoscopic procedures.