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In this paper a single particle/cell-tracking microfluidic device that integrates an out-of-plane multimode optical fiber (OP-MMF) is reported. This OP-MMF is used to generate three excitation light-lines and three detection spots using only one excitation source and one detector. It takes advantage of an optical tunneling mode to create two excitation lines in a microfluidic channel emanating from a single fiber end. This method was used to accurately count particles/cells and perform velocity measurements and size discrimination. The velocity and size distributions of 5, 7, and 10 μm fluorescently labeled polystyrene beads were determined using the OP-MMF. Additionally, this method was used to analyze cell lysates with the third excitation line in the separation channel. The OP-MMF setup accurately detected an intact cell twice ∼2 mm prior to lysis, determined its velocity, and detected the injected cell lysate 3 mm downstream of the injection point in the separation channel. Using this setup, the velocity of cells entering the lysis intersection and the absolute migration times of fluorescently labeled analytes injected into the separation channel were determined in an automated fashion. This method enabled us to determine a lysing/injection efficiency coefficient (K) using signals from the injected lysate signal and from the intact cell before lysing. K provided a reliable measurement of the amount of cell lysate that was injected into the separation channel. The approach reported here could be used in the future to track particles, cells or droplets in a variety of existing microfluidic devices without the need for multiplexed masks, layers, bulky optical elements or complex optical designs.