Because of the multifactorial nature of many diseases, two-dimensional electrophoresis is a basic proteomics tool for its ability of simultaneously detecting post-and co-translational modifications, which cannot be predicted from genome sequences.This review describes the central role of proteomics tool, two-dimensional electrophoresis for clinical biomarker discovery, the identification of prognostic and diagnostic markers, their use in monitoring the effects of drug treatments and eventually finding more efficient and safer therapeutics for a wide range of pathologies.