Recent development of protein microarrays and protein chips is allowing high-throughput analysis of proteins and/or molecules interacting with proteins. Powerful new technologies have currently been reported, which range from synthetic peptide arrays to whole cell protein arrays. Protein chips have been used in various applications for detecting interactions between enzyme-substrate, synthetic molecules-protein and different kinds of protein-protein. Such studies demonstrated that protein chips can be used to examine the functions of thousands of proteins in parallel in a single experiment. This review describes the development of protein microarrays and their potential applications in biological research, medicine and diagnostics.