This work describes a novel microfluidic device using a thin film transistor (TFT) photosensor integrating a microfluidic channel, a DNA chip platform, and a photodetector for the discrimination of single nucleotide polymorphisms (SNPs). A DNA-arrayed TFT photosensor was used as a DNA chip platform and photo detecting device. Chemiluminescence was used for DNA sensing because chemiluminescence provides higher sensitivity and requires simpler instrumentation than fluorescence methods. The SNP of biotinylated target DNA was detected based on chemiluminescence by using horse radish peroxidase-conjugated streptavidin. The lower detection limit for a model biotinylated oligonucleotide (63-mer) was 0.5 nM, much lower than expected DNA concentrations in a practical application of this device. Furthermore, SNP detection in the aldehyde dehydrogenase 2 gene was successfully achieved using DNA-arrayed TFT photosensor without DNA extraction and DNA purification using PCR products. The assay was completed in less than one hour. Our technology will be a promising approach to developing a miniaturized, disposable DNA chip with high sensitivity.