Capillary electrophoresis (CE) and related technologies have been utilized with great success for a variety of bioanalytical applications. CE has the advantages of decreased analysis time, integrated sample processing, high portability, high throughput, and minimal reagent consumption. Micro fabricated fluidic devices have also gained considerable interests due to its miniaturization and high level of integration. The goal of my research projects was to develop an integrated microfluidic system and technologies to perform in vitro and in vivo analysis of biological samples via electrophoretic separations. This dissertation focuses on the construction of flow-gated capillary electrophoresis systems and the development of related technologies coupled with laser induced fluorescence detection (CE-LIF) for rapid separation and sensitive detection of important components in biological samples. This dissertation first presents a custom-made PDMS-interconnected flow-gated CE system targeting on measurements of essential neurotransmitters. Experimental results show that this system was capable of performing long-term measurements with reproducibility, accuracy, sensitivity and robustness. Then, a novel and simple on-line sample preconcentration method was developed exclusively for enriching fluorescent derivatives of catecholamines, including dopamine and norepinephrine. The detection enhancement of over 100 folds was obtained and the limits of detection were lowered to the pico-molar range. Finally, a rapid and sensitive method was developed for the determination of cyanide ions in human urine, which is suitable for real-world applications, such as early diagnosis of cyanide exposure.