Traditional Chinese Medicine (TCM) is characterized with complexity and holism in both diagnostic and therapeutic principles.TCM prescriptions,termed as Fangji (formulas),generally consist of multiple Chinese medicine materials and each component also contains a large number of natural compounds.It makes the functional investigation of TCM difficult to perform with conventional assays.Recent advances in systems biology,particularly the high-throughput functional genomic tools,have paved the way to characterize the multiple gene and pathway targets of TCM for the interpretation of their functional mechanisms.In the meantime,it allows us to unravel the novel efficacy as well as possible side-effects of large number of TCM compounds,which will contribute to formulating a more potent therapy with high safety for different human diseases.