Proteomics has stimulated the development of very powerful methods for protein analysis. Implementation of some of these methods in clinical chemistry laboratories could offer clinicians better tools for diagnosis, prognosis and therapeutic follow-up of human diseases. However, laboratory medicine activities are bound by a number of constraints and rules for ensuring quality of results for clinical practice. There is therefore a gap to be filled between the research and routine medical laboratories. In this opinion article, we present the proteomic methods that will most likely be implemented in clinical chemistry laboratories in the short term, and we discuss the major issues yet to be addressed before considering such a transfer.