In the postgenomic era, the contents of methodology of human genomics researching is similar to the views of holism and syndromes differentiation of traditional Chinese medicine. So far, many scholars have probed beneficially into the essence of syndrome on the gene level. Since the syndrome of TCM have close intrinsic relations with not only the difference of gene expression but also the gene polymorphisms, therefore, it is capable, taking this as a cut-in point, to clarify the essential of syndrome by fully applying the advanced experimental methods and detecting techniques to deeply investigate the gene difference expression spectra based on the study of the relationship between gene polymorphisms and syndrome susceptibility, and analyze the regulatory network of the related genes from the view of functional genomics.