DNA microarray analyzes genome-wide gene expression patterns and is used in many areas including drug discovery and clinical applications. This chapter summarizes some of these applications such as identification and validation of anti-infective drug target, study mechanisms of drug action and drug metabolism, classification of different types of tumors, and use of molecular signatures for prediction of disease outcome. A step-by-step protocol is provided for sample preparation, sample labeling and purification, hybridization and washing, feature extraction, and data analysis. Important considerations for a successful experiment are also discussed with emphasis on drug discovery and clinical applications. Finally, a clinical study is presented as an example to illustrate how DNA microarray technology can be used to identify gene signatures, and to demonstrate the promise of DNA microarray as a clinical tool.