Pyrolysis mass spectrometry (PyMS) was used as a method of rapid inter-strain comparison of 19 isolates of coagulase-negative staphylococci from episodes of CAPD peritonitis. Thirteen isolates were from multiple, but distinct, episodes of peritonitis in 6 patients and the remaining 6 isolates were from 6 patients with single episodes. The results, expressed in terms of identity/non-identity of strains, were compared with those obtained using an established typing system comprising an extended antibiogram, determination of biotype and plasmid profile analysis. The PyMS results for inter-strain comparison were in agreement with the reference typing scheme results. PyMS can be used in this setting to rapidly obtain evidence that persistent infection is/is not likely to be due to the same organism, although it cannot be used for formal typing. The results by both methods showed that serial, apparently distinct, episodes of peritonitis over periods as long as 120 days may be due to the same strain of coagulase-negative staphylococcus. Clinically based distinctions between recurrence of infection (same strain) and re-infection (different strains) may not always be supported by the microbiological evidence.