There is a recent and growing interest in microscale separation and analysis, a result of advantages of miniaturization such as rapid separation times, high performance and throughput, reduced costs, and the possibility of system integration and multiplexing. Adopting the concepts of conventional capillary electrophoresis, capillary electrochromatography, micellar electrokinetic chromatography and various sample preparation techniques to microchip format, in conjunction with the integration of different analysis steps into a monolithic system, have opened new levels in performance, functionality and throughput. This review summarizes the recent advances in the field of microfabricated separation devices for genomics, proteomics and high-throughput screening applications, also addressing system integration and micropreparative functionalities.