Technology surrounding genomics, or the study of an organism's genome and its gene use, has advanced rapidly resulting in an abundance of readily available genomic data. Although genomics is extremely valuable, proteins are ultimately responsible for controlling most aspects of cellular function. The field of proteomics, or the study of the full array of proteins produced by an organism, has become the premier arena for the identification and characterization of proteins. Yet the task of characterizing a proteomic profile is more complex, in part because many unique proteins can be produced by the same gene product and because proteins have more diverse chemical structures making sequencing and identification more difficult. Proteomic profiles of a particular organism, tissue or cell are influenced by a variety of environmental stimuli, including those brought on by infectious disease. The intent of this review is to highlight applications of proteomics used in the study of pathogenesis, etiology and pathology of infectious disorders. While many infectious agents have been the target of proteomic studies, this review will focus on those infectious diseases which rank among the highest in worldwide mortalities, such as HIV/AIDS, tuberculosis, malaria, measles, and hepatitis.