Micellar electrokinetic chromatography (MEKC), combined with on-line concentration techniques, cation-selective exhaustive injection (CSEI) and sweeping, was developed for the analysis of cotinine, the primary biomarker for exposure to secondhand smoke. Experimental parameters including sample matrix, surfactant concentration, injection length and concentration of high-conductivity buffer, and sample electrokinetic injection time were optimized for electrophoretic enrichment and separation processes. Under the optimal conditions, the detection sensitivity of cotinine was enhanced by about 5000-fold using CSEI-sweeping MEKC compared to normal MEKC. The limit of detection for cotinine was found to be 0.2 ng/mL using ultraviolet absorbance detection. Furthermore, the developed method was successfully applied to the detection of cotinine in mouse serum samples.