Recent advances in the technology of massive parallel gene expression profiling using microarrays are revolutionizing biomedical research and pharmacological discovery. These new and powerful tools allow researchers to examine the dynamics of a whole biological system by simultaneously interrogating the expression of tens of thousands of genes. This article will review the various bioinformatics and statistical methods commonly used to analyze the enormous amounts of data generated by this technology. The objective of these analyses is to reliably extract important biological information from carefully designed and controlled microarray experiments, and to organize the information in ways that reveal structured and coordinated physiological processes and key components controlling the biological responses studied. The major applications of the microarray technology, recently used to address a variety of biological questions of interest to scientists and clinicians in academia, healthcare and the pharmaceutical industry, will also be presented.