To our knowledge, no previous study has addressed the question of which method of evaluation of the lower gastrointestinal tract is preferred by patients, air-contrast barium enema or colonoscopy. Over a four-month period, we asked 189 consecutive patients who had undergone colonoscopy to express their preference for either air-contrast barium enema or colonoscopy. A clear preference for colonoscopy was expressed by our patients in terms of comfort and polyp detection despite higher cost. Time lost from work and post-procedure constipation were significantly less for colonoscopy than for barium enema. These factors should be considered in the evaluation of suspected lower gastrointestinal tract disease.