A chemical marker of bacterial meningitis was sought by comparing derivatives of sterile cerebrospinal fluid (CSF) with cultures of organisms in spinal fluid and artificial media. The technique of gas chromatography-mass spectrometry with selected ion monitoring (GC-MS-SIM) was used, optimised for the analysis of fatty acids. Twenty candidate ions were screened, and an ion of mass: charge ratio (m/e) 268 was chosen for detection in clinical specimens. The origin of this marker is unknown, but it is probably the molecular ion of a C16:1 fatty acid. In 135 clinical specimens of CSF examined, the m/e 268 ion was found to be a useful marker for the common organisms that cause bacterial meningitis, giving a sensitivity of 88% and a specificity of 98%. The method was more rapid and more sensitive than conventional microscopy and culture, but CSF containing coagulase-negative staphylococci, Mycobacterium tuberculosis, Cryptococcus neoformans and some other uncommon pathogens gave inconsistent results. Many organisms produced characteristic ion profiles with multiple-ion monitoring, and this method of chemical analysis holds promise for the rapid diagnosis of bacterial infections to genus or species level.