Fueled by the identification and invention of novel gene delivery vectors, gene therapy efforts now hold promise for treating a wide range of diseases and are seen as a crucial part of growth for the biopharmaceutical industry. Currently, recombinant adeno-associated virus vectors (rAAVs) and lentiviral vectors (LVs) are the main vectors used in gene therapies that are approved or tested in human clinical trials. Meanwhile, ongoing research continuously reveals unprecedented knowledge of viral vectors on the host genome, which may subsequently affect the mutagenic and carcinogenic potential of these therapies. This article summarizes the content and addresses the commentary from the scientific symposium entitled “Mutagenesis and Carcinogenesis Risk Evaluation for AAV and Lentiviral Gene Therapies,” conducted at the 43 rd Annual Meeting of the American College of Toxicology, November 2022 in Denver, CO. The objective is to summarize the current understanding of rAAV and LV related mutagenicity/carcinogenicity risk, describe the methods and interpretation of results to guide risk assessments, as well as the current regulatory landscape on the carcinogenicity and mutagenicity assessment of rAAV and LV gene therapy products.