Lab-on-a-chip is a miniaturized analytical device in which all of the procedures for the analysis of molecules are carried out, such as pretreatment, reaction, separation, detection, etc. Lab-on-a-chip has increasing concern as a device not only for rapid detection of molecules but also for high throughput screening and point of care, because conventional laborious and time consuming analytical procedures can be substituted. Thus, a lot of microfabrication and analytical techniques for lab-on-a-chip have been developed with microstructures smaller than a few hundreds of micrometers. Separation of the molecules is one of the most important components of lab-on-a-chip, because effective separation method can simplify the design and can provide better sensitivity. The electrokinetic separation based on capillary electrophoresis is most widely employed technique in lab-on-a-chip for the control of fluids and the separation of molecules. In this article, bioseparation techniques and its applications realized in lab-on-a-chip are reviewed.