We report on the development of an inexpensive, portable lab-on-a-chip flow cytometer system in which microfluidics, photonics, and acoustics are integrated together to work synergistically. The system relies on fluid-filled two-dimensional on-chip photonic components such as lenses, apertures, and slab waveguides to allow for illumination laser beam shaping, light scattering and fluorescence signal detection. Both scattered and fluorescent lights are detected by photodetectors after being collected and guided by the on-chip optics components (e.g. lenses and waveguides). The detected light signal is imported and amplified in real time and triggers the piezoelectric actuator so that the targeted samples are directed into desired reservoir for subsequent advanced analysis. The real-time, closed-loop control system is developed with field-programmable-gate-array (FPGA) implementation. The system enables high-throughput (1-10kHz operation), high reliability and low-powered (<1mW) fluorescence activated cell sorting (FACS) on a chip. The microfabricated flow cytometer can potentially be used as a portable, inexpensive point-of-care device in resource poor environments.