Abstract: OBJECTIVE To predict the genotoxicity of organic impurities in materials of rivaroxaban and classify the genotoxicity, so as to provide a basis for the establishment of quality assurance system in actual production. METHODS The synthetic process of rivaroxaban was analyzed, and the possible organic impurities were speculated based on the production process that possible used in actual production. According to the internationally recognized guidelines, two complementary (quantitative) structure-activity relationships (Q)SAR prediction software based on expert knowledge rules and statistical rules were used to predict 18 organic compounds. The genotoxicity of impurities was predicted and classified according to their mutagenicity and carcinogenicity. RESULTS The 18 organic impurities, 5 were required to be controlled as genotoxic impurities and 13 as non-genotoxic impurities. CONCLUSION (Q)SAR can be used to evaluate the genotoxicity of related substances, which can quickly predict the characteristics of impurities. The prediction results indicate that rivaroxaban should establish effective quality control system for five impurities with warning structure of genotoxicity.