Vaccination is an effective means for prevention of the progression and spread of influenza virus infection. Nonetheless, there is a risk of adverse reactions, such as pain and fever, during the vaccination. In addition, because people from a wide age range, that is, from children to the elderly, are inoculated with vaccines, safety confirmation of these vaccines is important. Safety assessments of a vaccine, in the form of quality controls, have been carried out on animals. For example, the abnormal toxicity test is based on body weight changes as a toxicity index, and the leukopenic toxicity test can evaluate hematological toxicity. Meanwhile, since the 2000s, safety evaluation of drugs and chemicals by the genomic approach has been conducted frequently. The benefits with respect to safety evaluation are high sensitivity and abundant information about toxicity profiles. In this chapter, we describe the genes that are helpful as safety assessment markers and their usefulness for safety testing and vaccine development. In addition, this information may provide toxicity profiles, help understand the reactogenicity of nasal vaccines or adjuvants, and explain the prospects of genomic analyses in the development of novel vaccines and adjuvants.