A spectral-multiplexed fluorescence contact imaging microsystem for DNA analysis is presented. The microsystem integrates a filterless CMOS Color PhotoGate (CPG) sensor that exploits the polysilicon gate as an optical filter, and therefore does not require an external color filter. The CPG is applied to fluorescence-based transduction in a spectrally multiplexed format by differentiating among multiple emission bands, hence replacing the functionality of a bank of emission filters. A microsystem has been quantitatively modeled and prototyped based on the CPG fabricated in a standard 0.35 μm CMOS technology. The multi-color imaging capability of the microsystem in analyzing DNA targets has been validated in the detection of marker gene sequences for spinal muscular atropy disease and Escherichia coli (E. coli). Spectral-multiplexing enables the two DNA targets to be simultaneously detected with a measured detection limits of 240 nM and 210 nM for the two target concentrations at a sample volume of 10 μL for the green and red transduction channels, respectively.