DNA microarrays have provided researchers with a tool to detect differential expression of thousands of genes in a small sample and have clearly revolutionized the way gene expression analysis is now carried out. These microarrays are, however, confined to the detection of gene transcripts and do not permit the analysis of the translational product. This limits their potential use in research, since, after all, proteins are the business end of gene expression and the usual target of drugs. Until recently, protein detection strategies included ELISAs, Western blotting and immunohistochemistry, and were limited to the detection of a couple of proteins of interest. The recent development of protein microarrays now offers the possibility to simultaneously analyze the protein expression of several hundred proteins. Protein arrays allow us to measure the presence, biochemical characteristics and activation state of a considerable number of proteins in a single experiment. However, the formation of complex tertiary/quaternary structures and the interactions between many proteins still pose a veritable challenge for the development of high-throughput protein analysis, which might ultimately allow for the expression analysis of the whole proteome. In this review, we discuss the principle of antibody arrays and pay specific attention to the methodology of different array types. We also present a number of studies that have already shown the clinical utility of high-throughput protein assays, and which exemplify potential applications for this young and extremely promising technology.