A novel, FT-IR spectroscopic approach to the differentiation and identification of pathogenic microorganisms could be elaborated. The method takes advantage of the Fourier transform mid-infrared spectra of intact microorganisms. Such spectra could be recorded within minutes with high sensitivity and reproducibility when applying a highly standardized experimental procedure prior to ir measurements. By comparing the complete ir spectra - or selected spectral ranges of them - on the basis of their first and second derivatives, differentiation and identification of the microorganisms could be accomplished using cross-correlation algorithms.