DNA microarrays are high-throughput platforms that take advantage of the vast amount of sequence information and allow scientists to perform gene expression profiling or genotyping studies on a “global” or “genomewide” scale. The global monitoring of gene expression in hosts and pathogens, either separately or interactively, has given us systemic views of the disease mechanisms. Ongoing improvements in DNA sequencing and microarray technologies continue to open up new opportunities for better understanding and developing more effective approaches in diagnosis, treatments, and preventions of infectious diseases. This review focuses on the latest developments and applications of the DNA microarray technologies designed for studying pathogens in the areas of pathogenesis, host-pathogen interaction, drug response, vaccine development, and disease agent identification. Issues and challenges in the analysis, management and interpretation of microarray data are also addressed.