This article reviews recent capillary electrophoresis (CE)-based assays which were published for pharmacokinetic studies. Both the advantages and disadvantages of these CE-based assays are discussed based on their feasibility and the significance towards the better understanding of pharmacokinetics. In addition, as a future outlook, novel assays such as immunoaffinity CE and chip-based CE for analyzing drugs in biological fluids are summarized in view of their potential for pharmacokinetic applications.