We have developed a microfabricated fluorescence-activated cell sorter system using a thermoreversible gelation polymer (TGP) as a switching valve. The glass sorter chip has Y-shaped microchannels with one inlet and two outlets. A biological specimen containing fluorescently labeled cells is mixed with a solution containing a thermoreversible sol-gel polymer. The mixed solution is then introduced into the sorter chip through the inlet. The sol-gel transformation was locally induced by site-directed infrared laser irradiation to plug one of the outlets. The fluorescently labeled target cells were detected with sensitive fluorescence microscopy. In the absence of a fluorescence signal, the collection channel is plugged through laser irradiation of the TGP and the specimens are directed to the waste channel. Upon detection of a fluorescence signal from the target cells, the laser beam is then used to plug the waste channel, allowing the fluorescent cells to be channeled into the collection reservoir. The response time of the sol-gel transformation was 3 ms, and a flow switching time of 120 ms was achieved. Using this system, we have demonstrated the sorting of fluorescent microspheres and Escherichia coli cells expressing fluorescent proteins. These cells were found to be viable after extraction from the sorting system, indicating no damage to the cells.