The potential clinical application of gas chromatography to microbial identifcation was evaluated. A completely automated system, the MIS (Microbial Identification System; Hewlett- Packard) can analyse and identify pure strains by comparison of their cellular fatty acids patterns (C9-C20) with the reference parameters stored in a library. Three hundred and sixty-seven strains were tested, comparing the gas chromatographic results with those obtained by the traditional microbiological methods in the bacteriology laboratory of our Institute. A standardized extractive procedure was followed to obtain the fatty acid methyl esters (FAMEs), but some modifications to the recommended procedure were introduced in the bacterial growth procedures: colonies harvested not only from the recommended growth media but also from selective media routinely used in the bacteriology laboratory were successfully examined. These modifications did not influence the results but improved the ease for the user; good agreement with the comparison method was observed as far as identifications of genus and species are concerned for 238 cases. The major advantages of this computerized system are a reduction in the time required to obtain the final results, the elimination of human errors by using the autosampler and a better inter-laboratory comparability of results owing to a higher degree of objectivity. On the other hand, the limited throughput of MIS (only 40 samples in 24 h) prevents its use in a large routine laboratory; this technology is appropriate in emergency cases, in taxonomic studies and as a confirmatory method.