DNA microarray technology offers a new way to clinical diagnostics involving biomarker discovery and disease diagnosis. DNA microarray can be used for diagnosis of pathogens by analyzing hybridization patterns between capture probes and nucleic acids isolated from clinical samples. It allows more rapid, accurate, and cost-effective detection of pathogens compared with traditional approaches of cultivation- or immuno-assays. As infectious diseases are posing more serious threats to public health care, development of a rapid and accurate method for pathogen detection is critical to the proper treatment of infected patients at the earliest time. Here we review recent patents on the use of DNA microarray for diagnosing pathogens.