This research paper presents a new high throughput comet chip platform for assessing DNA damage in cells induced by engineered nanoparticle exposure. Various nanoparticles were synthesized and characterized. Cells were exposed to different concentrations of nanoparticles and evaluated for DNA damage using both the comet chip platform and traditional comet assay. The comet chip approach allowed for automated, high throughput analysis of DNA damage and was found to produce robust data while being more efficient than traditional comet assay. Significant single stranded DNA damage was observed in cells exposed to zinc oxide nanoparticles. The comet chip platform shows potential as an improved method for predicting nanoparticle genotoxicity.