We report a new microfluidic cell sorting system for early diagnosis of genitourinary cancer based on photodynamic analysis of urine. In the developed system, genitourinary cancer cells are detected using 5-aminolevulinic acid (5-ALA)-induced fluorescence and then sorted for gene alteration analysis. The unique characteristic of this cell sorter is that the microchannel's microstructure is fabricated using one-step UV photolithography, to create a disposable, low-cost device that has low autofluorescence. In this paper, we examine the performance of the microfluidic cell sorting system for diagnosing genitourinary cancer, and evaluate the accuracy of cancer cell separation when using the 5-ALA treatment, and also when using fluorescent beads.