The beneficial physiological effects of food and fragrances have been increasingly focused in recent years. The extensive use of fragrances is being promoted in the fields of food, cosmetics, health, and pharmaceutical sciences. The launch of the system of Foods with Function Claims in 2015 further enhanced the interest in the physiological effects of these components. However, there are many challenges in evaluating the physiological effects of fragrances in real-life conditions, and sufficient outcomes have not been obtained yet. Therefore, it might be important to identify problems in evaluation systems and develop or introduce new evaluation systems to promote the effective use of food and fragrances. Challenges and issues related to conventional methods of evaluation are discussed. Moreover, physiological techniques of comprehensive evaluation are presented with the aim of contributing to development of research on fragrances.