When confronted with a septic patient or dealing with an emerging epidemic, clinicians, infection control specialists and microbiologists have often felt an immense 'need for speed' while waiting for culture results. Various mass spectrometry (MS) applications are about to answer most of their demands. Matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) MS of whole bacterial cells has already greatly shortened the time needed for identification of a positive culture in major diagnostic laboratories in Europe. MS is described in this article, with a special emphasis on the different systems currently commercially available for routine identification. MALDI-TOF MS remains, however, limited by the previous time-consuming culture steps, and is not suited for strain typing in epidemic contexts. These limitations can be overcome by other applications of MS in microbiology. MALDI-resequencing is a rapid method for genotyping, offering comparable results to multilocus sequence typing. New systems of broad-range PCR, associated with analyses of amplicons by electrospray ionization MS, might allow nearly full automation for the direct identification of pathogens in blood, thus bypassing the culture stage. This article describes various applications of MS methods in clinical microbiology, and provides a comparative table of these technologies.