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Microarray technology is a high-throughput platform for the comprehensive analysis of gene expression on a whole genome scale. Most approaches use a solid phase surface to geographically fix specific gene probes and quantification is based on radiometric, fluorometric, or electrochemical detection of hybridized biomolecules such as RNA, DNA, or protein. The technique produces two-dimensional "images" of gene expression and has been discussed in the context of in vitro "molecular imaging". The major challenge in using this technology is the analysis of its massive "image" data output which requires computational means for interpretation, a heightened need for quality data, and precise experimental design. We will discuss the current technologies focused on nucleic-acid-based microarray platforms. This technology has been extended to the detection of DNA binding complexes, single nucleotide polymorphisms, and in DNA copy number assessment with reasonable success. The future focus will be on improving the probe density, array flexibility, and the dynamic range of detection of the technical platform. On a larger scale, data integration and visualization, and on the intelligent utilization of prior biologic information will be the computational challenge.