Traditional Chinese medicines (TCM) are a rich source of potential leads for drug development. However, there are fundamental differences between traditional Chinese medical concepts and modern pharmacology, which greatly hinder the modern development of TCM. To address this challenge, new techniques associated with genomics, transcriptomics, proteomics, metabolomics and bioinformatics have been used to dissect the pharmacological mechanisms of TCM. This review article provides an overview of the current research in this area, and illustrates the potential of omic and bioinformatic methods in TCM-based drug discovery.