Drug addiction, a chronic brain disease caused by interaction of in vitro drug toxification and in vivo gene susceptibility, has been widely studied but its underlining mechanism is so far been elucidated. A major goal in this field is to identify drug-induced molecular changes and their effects on brain function. By the advance of high throughput technologies in genomics and transcriptomics, the whole gene expression profile in addicted brain could be obtained and proved to be a very powerful tool to unclose the molecular mechanism underlying the addiction biology context. Here, we summarized the progress of serial analysis of gene expression (SAGE) and microarray, as well as their application in drug addiction.