Fast bacterial identification in urine samples was achieved by capturing bacteria on a microchannel silicon nanowire microfluidic chip, followed by MALDI-TOF MS detection. Under the optimized conditions, bacteria with a concentration of 106 CFU mL-1 in urine samples could be identified without culture. If cultured for 4 hours, bacteria with a concentration as low as 103 CFU mL-1 were identified.