Genomics and proteomics are playing increasingly important roles as discovery tools in basic biological sciences and as diagnostic and rational therapeutic aids in the clinical arena. In recent years, high-density arrays of specified DNA sequences have gained popularity. Protein microarrays are at the forefront of this biochip revolution and promise the parallel examination of large numbers of proteins. These miniaturized arrays are currently being developed to facilitate high analytical resolution, detection sensitivity and sample throughput. Many challenges are presented by proteome scale manipulation of proteins, as there is currently no methodological equivalent to the gene chip for comparative proteomics.