During the past 30 years, slab gel electrophoresis has been one of the most important tools available to modern biochemistry, biology, and clinical research. However, despite substantial progress in methodology, slab gel techniques typically suffer from laborious, time-consuming and difficult-to-automate procedures. Capillary electrophoresis (CE), first introduced a decade ago, emerges now as an alternative to slab gel techniques with all the advantages of modern automated technology. Although the first target of CE was analysis of small molecules (it is a highly efficient alternative to HPLC), now a main focus is on biopolymers. Currently, CE can be viewed as a fully automated tool for rapid, highly sensitive, and quantitative analysis of minute (nanoliter) amounts of complex samples. This chapter reviews the most important CE techniques and their use for the analysis and characterization of proteins and DNA.