Arterial blood oxygen desaturation and abnormal electrocardiographic changes have been reported in adults undergoing upper gastrointestinal endoscopy. We studied 32 infants and children less than 12 years of age using pulse oximetry and continuous electrocardiography before, during, and after upper gastrointestinal endoscopy performed under intravenous sedation. Sinus tachycardia was the most common electrocardiographic change, and no clinically significant electrocardiographic abnormalities were induced by the procedure. Desaturation to less than or equal to 90% was found in 37.5% of the patients and was most commonly noted during the endoscopy procedure and in patients with cardiopulmonary disease. The desaturation was unpredictable because there was no correlation between desaturation and medication, tolerance to the procedure, weight, or age of the child. Some patients who subjectively appeared to tolerate the procedure well had significant desaturation. The use of pulse oximetry should be considered for all children undergoing upper gastrointestinal endoscopy.