This paper presents a two-dimensional a–Si:H/a-SiC:H n–i–p photodiode array with switching diode readout, developed specifically for fluorescence-based bio-assays. Both device structure and fabrication processing has enabled enhancement of the external quantum efficiency of the encapsulated device up to 80%, reduction of the photodiode leakage down to 10 pA/cm2 at -1V reverse bias, and increase of the rectification current ratio of the switching diodes up to 109. The critical fabrication issues associated with deposition of device-quality materials, tailoring of defects at the i–p interface, device patterning with dry etching, junction passivation, and contact formation will be discussed. Both sensing and switching diodes were characterized. While the observed dark current in the photodiodes at low reverse bias voltages is primarily due to carrier emission from deep states in the a–Si:H bulk, the leakage in the small switching diodes stems from peripheral defects along junction sidewalls. Optical losses in the photodiodes with ITO/a–SiNx:H antireflection coating were evaluated using numerical modeling, and the calculated transmission spectra correlated well with the spectral response characteristics. Measurements of the charge transfer time and output linearity demonstrated the efficiency of the single-switching diode readout configuration. The response of the array to optical excitation was also investigated. The observed long term retardation in the signal rise and decay at illumination levels less than 1010 photons/cm2-s can be associated with charge trapping in the undoped layer.