Pharmacoproteomics is the use of proteomic technologies in drug discovery and development. Along with pharmacogenomics and pharmacogenetics, pharmacoproteomics will play an important role in the development of personalized medicines in several ways. Proteomic technologies are contributing to molecular diagnostics, which is the basis of personalized medicine. Pharmacoproteomics is a more functional representation of patient-to-patient variation than that provided by genotyping. Proteomics-based characterization of multifactorial diseases may help to match a particular target-based therapy to a particular marker in a subgroup of patients. Individualized therapy may be based on differential protein expression rather than a genetic polymorphism. Finally, proteomic technologies would enable the discovery and development of drugs suitable for personalized therapy. Protein chips will be used increasingly in clinical diagnostics in the next 5 years, particularly in the point-of-care diagnostics. This will facilitate the practice of personalized medicine in the clinic by the end of this decade.