We have shown the design and fabrication of a microfluidic flow cytometer. The microfluidic flow cytometer has been used to characterize microspheres of different sizes. The device is consisted of a microchannel, electronics, and integrated optics. The microchannel has three inlets. Two inlets are used to introduce sheath flows and one middle inlet is assigned as sample inlet. The sample flow is hydrodynamically focused at the center of the microchannel by two side streams (sheath flows). Also arrays of four chevron grooves compress the sample flow from the top and bottom of the microchannel. The core flow contains microspheres at a certain concentration. Detection of the microspheres at the interrogation region of the channel is performed by integrated optics and electronics. The scattered light emitted from the microspheres is collected by a multi-plex photo diode (MPPC). The results are recorded using data acquisition (DAQ) unit. The MPPCs employed in the setup is the new generation of photon counter devices with an excellent detection limit, a compact size, and capability of recording data at high gain compared to previous generation of photodetectors such as photomultipliers or avalanche photon diodes. The flow cytometer was sensitive enough to collect data from 3 μm microspheres using such mentioned sensitive photon counting unit. We have also used COMSOL Multiphysics software to investigate velocity and pressure distribution as well as concentration distribution along the microchannel. The average voltage collected by MPPC was 1.9 V for 10.2 μm and 1.6 V for 3.2 μm microsphere.