Objective To make comet assay automated and standardized; to study and test the function and reliability of comet auto-assay (Comet A) software. Methods Comet A software installed on 3 different computers were operated independently by 3 analysers to analyze the same 30 pieces of comet pictures; some pictures were also measured by visual scales. The results were analyzed and the functions of comet A software were tested. Results The results analyzed by 3 analysers independently were not significantly different from each other; there were no significant differences between the results analyzed by visual scale and Comet A. The functions of Comet A were auto selection and recognition, auto analysis, auto storage and traceable to the source. Conclusion The results analyzed by Comet A software are stable and reproducible, which is helpful to make comet assay automated and standardized.