Abstract Chinese herbal medicines have been used for the treatment of various diseases for centuries. Although several herbal formulas and herbal components have shown therapeutic potential, the active components and the molecular mechanisms mediating the effects of said formulas remain to be discovered. Microarray analysis has become a widely used tool for the generation of gene expression data on a genome-wide scale. This paper discusses the application of whole genome expression profiling as a tool to investigate the molecular mechanisms governing the therapeutic effects of traditional Chinese medicine. This review also highlights how data derived from DNA microarray analysis can be used to screen for drug targets of various herbal drugs, to predict the therapeutic potential of herbal drugs, to analyze the safety of drugs in the preclinical stage of drug development, and to establish a modern definition of traditional Chinese medicine.