Advances in the rapidly evolving discipline of pharmacogenomics have forced the biotechnology and pharmaceutical industries to integrate differential gene expression profiling into their drug discovery and development strategies. Here we highlight the use of differential gene expression technologies for the elucidation of both drug efficacy and toxicity as well as novel candidate genes for pharmacogenetic analyses to assess individual variability to drug response. This will include an overview of the different technologies created to facilitate pharmacogenomic analyses and to highlight advantages and disadvantages of these emerging methodologies. Two high-throughput differential gene expression technologies, microarrays and GeneCalling((R)), will be presented in detail.