The recent completion of the malaria parasite Plasmodium falciparum genome has opened the door for applying a variety of genomic-based systems biology approaches that complement existing gene-by-gene methods of investigation. Transcriptomic analyses of P. falciparum using DNA microarrays has allowed for the rapid elucidation of gene function, parasite drug response, and in vivo expression profiles, as well as general mechanisms guiding the parasite life cycle that are vital to disease pathogenesis. The results of these studies have identified promising novel gene targets for the development of new drug and vaccine therapies.