Poly(dimethylsiloxane) microfluidic channels alternately modified by poly(diallyldimethylammonium chloride) and poly(sodium 4-styrenesulfonate) were successfully used to separate uric acid and ascorbic acid. Results show that uric acid and ascorbic acid can be well separated and detected simultaneously in modified microchips coupled with in-channel electrochemical detection. Under the optimal conditions, the linear ranges of uric acid and ascorbic acid were both from 25 to 600 microM, with the correlation coefficients of 0.997 and 0.996, respectively. The detection limits were 8 microM for uric acid and 5 microM for ascorbic acid. Factors influencing separation and detection, including buffer solution, detection potential and separation voltage, were investigated and optimized. In addition, the dependences of the current response on sensitivity and reproducibility were studied, and the stability of the device was also evaluated in detail. This method was successfully used to determine uric acid and ascorbic acid in human urine.