Microfluidic inertial focusing has been shown as a simple and effective method to localize cells and particles within a flow cell for interrogation by an external optical system. To enable portable point of care optical cytometry, however, requires a reduction in the complexity of the large optical systems that are used in standard flow cytometers. Here, we present a new design that incorporates optical waveguides and focusing elements with an inertial focusing flow cell to make a compact robust cytometer capable of enumerating and discriminating beads, cells, and platelets.