AbstractFunctional protein microarrays are emerging as a promising new tool for large‐scale and high‐throughput studies. In this article, we review their applications in basic proteomics research, where various types of assays have been developed to probe binding activities to other biomolecules, such as proteins, DNA, RNA, small molecules, and glycans. We also report recent progress of using functional protein microarrays in profiling protein post‐translational modifications, including phosphorylation, ubiquitylation, acetylation, and nitrosylation. Finally, we discuss potential of functional protein microarrays in biomarker identification and clinical diagnostics. We strongly believe that functional protein microarrays will soon become an indispensible and invaluable tool in proteomics research and systems biology. WIREs Syst Biol Med 2011 3 255–268 DOI: 10.1002/wsbm.118This article is categorized under: Laboratory Methods and Technologies > Proteomics Methods