We studied the effects of fiberoptic upper intestinal endoscopy on blood oxygenation and cardiac rhythm in 13 patients. Six patients had normal pulmonary function or mild obstruction to air flow. None of these developed arterial oxygen desaturation during endoscopy. Seven patients had moderate to severe airflow obstruction. Six of these desaturated to less than 90%; the mean +/- SEM arterial oxygen tension changed from a baseline of 75 +/- 2 mm Hg to 54 +/- 2 mm Hg during endoscopy (P less than 0.01). Electrocardiographic changes during endoscopy occurred in 5 patients, 4 of whom had moderate to severe airflow obstruction. In 3 of these patients, the ECG changes were concurrent with desaturation. Patients with moderate to severe airflow obstruction frequently become hypoxemic and may develop cardiac arrhythmias during upper gastrointestinal endoscopy.