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The trend in medical equipment is toward compact and integrated low-cost medical test devices. Fluorescence-based assays are used to identify specific pathogens through the presence of dyes, but typically require specialized microscopes and narrowband optical filters to extract information. We present a novel, high-sensitivity, cost-effective, cross-polarization scheme to filter out excitation light from a fluorescent dye emission spectrum. This concept is demonstrated using an inverted microscope fitted with a halide lamp as the excitation source and an organic photo voltaic (organic photodiode) cell as the intensity detector. The excitation light is linearly polarized and used to illuminate a microfluidic device containing a 1 volume of dye dissolved in ethanol. The detector is shielded by a second polarizer, oriented orthogonally to the excitation light, thus reducing the magnitude of the detector photocurrent by about 25 dB. The signal due to fluorescence emission light, which is randomly polarized, is only attenuated by about 3 dB. As proof-of-principle, the fluorescence signal from the dyes Rhodamine 6G (emission wavelength of 570 nm) and Fluorescein (emission wavelength 514 nm) are measured in a dilution series with resulting emission signal being detected by an organic photodiode. Both dyes were detectable down to concentrations of 10 nM. This suggests that an integrated microfluidic device, with an organic photodiode and an organic light emitting excitation source and integrated polarizers, could be fabricated to realize compact and economical lab-on-a-chip devices for point-of-care diagnostics and on-site analysis.