The major application of MALDI-TOF mass spectrometry in clinical microbiology is the bacterial identification based on the analysis of all their proteins (ribosomal and membrane-associated proteins). This technology allows the identification of most of bacteria within a few minutes. The method is fast, accurate, reliable and cost-effective by comparison to conventional phenotypic techniques. Other applications of MALDI-TOF mass spectrometry are still under development, as the detection of bacterial toxins or resistance mechanisms to antimicrobial agents.