Eighteen isolates of Bacillus species and 15 of Clostridium perfringens, all of which had been associated with outbreaks of either food poisoning or non-gastrointestinal infection (NGI), were examined for relatedness by pyrolysis mass spectrometry (PyMS). The PyMS-analysis correctly clustered all the groups of epidemiologically related isolates of both genera, and distinguished all the single, epidemiologically unrelated isolates of the same species. PyMS is a simple, rapid and inexpensive technique which can provide useful and accurate inter-strain comparisons within both the Bacillus and Clostridium genera in complete accord with conventional serological typing results.