Proteomics is the science that studies the proteins in general and in particular their changes, resulting from various disorders or the effect of external factors, such as toxic agents. It has as goal the detection of novel drug targets, diagnostic markers and the investigation of biological events. Proteomics has emerged the last few years and its major difference from the previously existing protein analytical techniques is that it does not analyze the proteins one by one, but in a possibly automated, large-scale mode. In this article, the state of the art of proteomics in our laboratory is presented, as well as selected applications of proteomics in the study of disorders of the central nervous system and of toxic events.