Traditional Chinese medicine often clashes with contemporary medicine because its principles and concepts are difficult to understand to scientists with a background in contemporary medicine. Therefore, more proof and explanation of traditional Chinese medicine at the molecular level are necessary. Expression microarrays, among the most important genomics techniques in modern systems biology, can simultaneously detect the expression levels of thousands of genes and identify related gene networks in biological systems. They may connect gene expression at the microlevel and system information at the macrolevel together. Expression microarrays may create building blocks to bridge traditional Chinese medicine and contemporary medicine. They may not only identify the action (or toxicological) mechanism or active ingredients of Chinese herbal medicine but also reveal the molecular mechanism of traditional Chinese medicine theories. The following is a brief overview of some applications of expression microarrays for traditional Chinese medicine studies.