Following a case of Legionnaires' disease Legionella pneumophila of the same serogroup was isolated from the hot water system of the hotel which had been epidemiologically implicated as the source of the infection. Pyrolysis mass spectrometry (PyMS) was used to compare 11 isolates from the hotel water sample with the patient's strain. Epidemiologically unrelated isolates, both clinical and environmental, of the same serogroup and monoclonal antibody type of L. pneumophila were included in the same analysis, together with relevant reference strains. The patient strain was shown to be indistinguishable from seven of the hotel water isolates, but clearly different from other unrelated clinical isolates, the reference strains and some of the other environmental isolates. PyMS is a rapid and cheap method for inter-strain comparison for L. pneumophila.