The use of a method to follow changes in endogenous peptide production, as they occur in biological studies, is an excellent complement to other molecular techniques. It has the unique ability to characterize peptides that have been produced from protein precursors, and instrumentation is available that provides high resolution peptide separations that are quantitative, sensitive, and amenable to automation. All tissues express a large number of peptide species that can be visualized, or profiled, on chromatographic separations using reverse-phase high-performance liquid chromatography. This large number of peptides offers many potential molecules that can be used to identify biological mechanisms associated with experimental paradigms. Peptide analysis has been used successfully in many types of studies. In this review, we outline our experience in using peptides as biological markers and provide a description of the evolution of peptide profiling in our laboratories. Peptide expression has been used in studies ranging from how brain regions develop to identifying changes in disease processes including Alzheimer's disease and models of stroke. Some of the findings provided by these studies have been new pathways of peptide processing and the identification of accelerated proteolysis on proteins such as hemoglobin as a function of Alzheimer's disease and brain insult. Peptide profiling has also proven to be an excellent technique for studying many wellknown nervous system proteins including calmodulin, PEP-19, myelin basic protein, cytoskeletal proteins, and others. It is the purpose of this review to describe our experience using the technique and to highlight improvements that have added to the power of the approach. Peptide analysis and the expansion in the instrumentation that can detect peptides will no doubt make these types of studies a powerful addition to our molecular armamentarium for conducting biological studies.