Silk nanoparticles (SNPs) are effective and versatile protein-based systems for variety applications, such as targeted drug delivery and controlled release with their biocompatibility and highly functionalizable surface chemistry. Various methods have been used for the evaluation of toxicity in SNP-oriented systems. In particular, MTT assay and Comet assay are one of the commonly used cytotoxic and genotoxic methods, respectively. Although the mechanism of action of nanoparticles (NPs) on DNA and cells has not been clearly explained, it is evident that it is associated with an increase in the amount of ROS and apoptotic cell death. In addition, various parameters such as exposure dose, usage route, organ of action also affect its toxicology. In our article, we discussed the structure of SNPs, their suitability for bioapplications, toxicological effects, and usable doses from a broader perspective. We evaluated their applicability by presenting changes that can be made in the future to reduce their toxicology.