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The respiratory effect of diagnostic colonoscopy and upper endoscopy were studied in 32 elderly patients. Twenty-two underwent colonoscopy and 10 upper endoscopy. In the group undergoing upper endoscopy, 4 of 10 patients experienced a decrease in oxygen desaturation greater than or equal to 4% during the medication period; an additional 2 patients desaturated during the procedure. In the group undergoing colonoscopy, 12 of 22 patients experienced oxygen desaturation during the medication period; 3 other patients desaturated during the procedure. Mean SaO2 for each group was lowest (p less than 0.05) during the medication period. Central apneas occurred in 13 of the patients undergoing colonoscopy during the medication period; however, only 8 of these patients with apneas experienced desaturation greater than or equal to 4% and the periods of desaturation did not correlate with the periods of apneas. Oxygen desaturation greater than or equal to 4% occurs frequently during both upper endoscopy and colonoscopy in this elderly population. This is related to the effects of sedation; the procedure itself worsened the desaturation in only 16% of the patients. Furthermore, the desaturation did not correlate with changes in the breathing patterns of the patients. Low-flow oxygen and/or close monitoring of patients during and subsequent to administration of medication is advised.