This study was designed to compare the effects of alfentanil and midazolam pre-medication on patient comfort during and after flexible bronchoscopy. A randomised, double-blind study was performed; 40 patients received alfentanil and 29 midazolam. Subjects completed questionnaires about discomfort and adverse effects immediately post-procedure and 24 h later. The bronchoscopist also completed a questionnaire. No difference in patient discomfort was found immediately post-procedure and no differences were found for amount of topical lignocaine used or minimum oxygen saturation. Operators reported no overall difference between the agents for ease of procedure but about 20% less cough was reported in the alfentanil group (P = 0.02). Patient discomfort scores in the 24h questionnaire were significantly lower in patients given midazolam (P = 0.01 for nasal discomfort, P = 0.003 for throat discomfort) but drowsiness was commoner in this group (P = 0.04). There was no significant difference in patients' reports of cough, nausea or vomiting or their willingness to have a repeat procedure. In conclusion, cough during bronchoscopy was slightly less marked with alfentanil than midazolam pre-medication but this made no difference to the ease of procedure or to overall patient discomfort. Patients given midazolam reported less discomfort when asked about the test 24 h later.