Vaccines effectively prevent infectious diseases. Many types of vaccines against various pathogens that threaten humans are currently in widespread use. Recently, adjuvant adaptation has been attempted to activate innate immunity to enhance the effectiveness of vaccines. The effectiveness of adjuvants for vaccinations has been demonstrated in many animal models and clinical trials. Although a highly potent adjuvant tends to have high effectiveness, it also has the potential to increase the risk of side effects such as pain, edema, and fever. Indeed, highly effective adjuvants, such as poly(I:C), have not been clinically applied due to their high risks of toxicity in humans. Therefore, the task in the field of adjuvant development is to clinically apply highly effective and non- or low-toxic adjuvant-containing vaccines. To resolve this issue, it is essential to ensure a low risk of side effects and the high efficacy of an adjuvant in the early developmental phases. This review summarizes the theory and history of the current safety assessment methods for adjuvants, using the inactivated influenza vaccine as a model. Our novel method was developed as a system to judge the safety of a candidate compound using biomarkers identified by genomic technology and statistical tools. A systematic safety assessment tool for adjuvants would be of great use for predicting toxicity during novel adjuvant development, screening, and quality control.