This manuscript reports the conclusions of a working group of the French Society of Clinical Biology (SFBC) 2007-2008 which evaluated the status, the impact and the future developments related to the analysis of the proteome using multiplexed methods. These approaches that are also used in clinical biology are performed on solid supports or in flow by using specifically dedicated or conventional flow cytometers. This review provides therefore a broad overview going from the methods already present in research laboratories to the tools for clinical and medical investigations.