The advent of molecular technologies that allow the collection and analysis of large amounts of genetic data is rapidly transforming the field of genetic epidemiology. Whether monitoring infectious outbreaks or identifying genotypic variations that underlie disease susceptibility, genetic epidemiology relies heavily on the analysis of multiple, independently derived results. By allowing the simultaneous monitoring of thousands of genetic or expression data points, microarrays are emerging as particularly powerful tools. Several recent reviews have described array manufacturing and the types of scientific questions that can exploit this technology, but few have addressed how the intended use of an array can dictate its design. This review will focus on this latter issue, with particular emphasis on the genetic epidemiology of infectious disease. The design of arrays for genotyping, expression profiling, and fingerprinting are presented, and examples of recent epidemiological studies are used to illustrate the applications' strong points and limitations. In addition to discussing arrays' ability to provide global views of gene identity or function, the review will describe design options for creating arrays that detect multiple genetic variations. It will also examine the reliability of array-generated fingerprints, assay accessibility, and possibilities for sharing and comparing data across studies. Although many challenges lie ahead, microarrays' multiple abilities appear uniquely poised to accelerate the advance of genetic epidemiology's multiple fronts.