IR spectra of intact microbial cells are fingerprint-like signatures which provide multi-dimensional information on cell composition and structure. These spectral signatures are already used in practice to identify divers microbial species and strains, to characterize particular cell compounds in situ, and to monitor cell-drug interactions. New applications arise by means of a light microspace coupled to the IR spectrometer: IR-spectra of micro-colonies containing a few hundred cells can be obtained from colony replica by a stamping technique that transfers spatially accurate micro-colonies growing on solid culture plates to a special, IR-transparent stamping device. Using a computer controlled x, y stage together with spectral mapping and video techniques, detection, enumeration, and differentiation of micro-organisms are integrated in one single apparatus, providing diagnostic results within one working day. Additional items of the new are integrated in one single apparatus, providing diagnostic result within one working day. Additional items of the new approach are (i) rapid sensitivity and resistance testing against various antimicrobial drugs, and (ii) the conductance of spectral mapping analysis on single colonies enabling the spatially resolved characterization of growth heterogeneity within complex populations of micro-organisms.