Protein microarrays, also known as protein chips that provide a unique platform for characterization of thousands of proteins in a highly parallel and high-throughput way. Two major classes of protein microarrays are defined. They are analytical and functional protein microarrays. Analytical protein microarrays, mostly antibody microarrays, have become one of the most powerful multiplexed detection technologies. Functional protein microarrays are being increasingly applied to many areas of biological discovery, including studies of protein interaction, biochemical activity, and immune responses.