Vaccines are the most effective tool to prevent and control infectious diseases in humans and will remain a major tool for combatting unknown infectious diseases that emerge in the future. Recent advances in vaccinology, combined with molecular biology and immunology, enable us to develop well-designed vaccines to induce target-oriented immunity without using conventional vaccine production platforms, such as the inactivation of live pathogens and splitting their components. On the other hand, assessment of vaccine safety at the preclinical level and after the licensure have not changed since preclinical and lot release testing were introduced 50 years ago. Our laboratory has been committed to investigating the potential safety of newly developed vaccines and assuring the lot-to-lot consistency of vaccines as a national control laboratory. Herein, we introduced our new assessment tool for vaccine safety and quality control. Systems vaccinology approaches enable us to identify potent biomarkers (BMs) for evaluating the safety of influenza vaccines and adjuvants administered via any in vivo injection route in mouse models. Some parts of BMs could be applied or extrapolate for humans using in vitro human peripheral blood mononuclear cell models and in vivo humanized mouse models. Taken together, our findings could allow us to bring next-generation safety evaluations of vaccines and adjuvants.