Separations of human urine by microemulsion electrokinetic chromatography (MEEKC) and micellar electrokinetic capillary chromatography (MEKC) with respect to resolution, migration times and efficiencies were optimized and compared. The optimised MEEKC and MEKC methods were simple and fast, both of which are excellent characteristics for the complex separations required in clinical and biomedical studies. However, resolution in MEKC was significantly greater than in MEEKC although migration times were 30% faster for the optimised MEEKC method. In addition, a faster analysis method (short-end injection) specifically for routine screening purposes was also investigated. With both MEEKC and MEKC modes, this provided short separations (less than 4 min for urine) with no major compromise in resolution. In conclusion, we found that MEEKC offered no real advantage over MEKC for urine analysis.