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A simple amplified fragment length polymorphism method was developed for the epidemiological typing of Bacillus cereus. The method was applied to 21 cultures from seven food poisoning and eight non-food poisoning incidents. Results were compared with those obtained by conventional serotyping using flagellar antigens and assessed in relation to epidemiological data. Amplified fragment length polymorphism was found to be highly reproducible and 16 different profiles (each unique to the 15 incidents) were recognized. The method was also able to discriminate three subtypes within serotype H1, which is responsible for the majority of the emetic type of B. cereus food poisoning in England and Wales.