Many antibiotic regimens for treating Helicobacter pylori infection are currently used in clinical trials. The reported side-effect profiles of similar anti-Helicobacter therapies vary widely due to the use of different scoring systems. Therefore side-effect data from separate studies cannot be compared. Only randomized controlled trials will show how side-effect profiles and tolerability really differ between regimens, but few such studies are available. Therefore a choice of treatment based on side-effect profile is not possible at present. We seek standardization of side-effect registration among investigators and propose a side-effect questionnaire which, if generally accepted, would make it possible to compare data between trials.