The Organization for Pharmaceutical Safety and Research (OPSR), Pharmaceuticals and Medical Devices Evaluation Center (PMDEC), National Institute of Health Sciences and Ministry of Health, Labour, and Welfare (MHLW) are working together on the new pharmaceutical approval process in Japan for appropriate scientific approaches. The Consultation Division of OPSR helps the pharmaceutical companies to answer find solutions to their concerns about non-clinical and clinical trials in the new pharmaceutical development process. After a new pharmaceutical application, PMDEC evaluates the quality, efficacy, and safety of each pharmaceutical compound in the review process. Final judgment for approval is made by MHLW. Pharmacological mechanisms examined in non-clinical trials would be useful for selection of the appropriate end-point in the clinical trials. For safety assessment, International Conference of Harmonization (ICH) Guideline on Safety Pharmacology Studies was officially notified. According to pharmacological data on safety, clinical investigators can better design clinical trials to prevent patients from suffering serious adverse events. To development new epoch pharmaceuticals, continuous progress on pharmacological research will be indispensable. Further discussion among all interested parties such as pharmacological researchers, medical doctors, companies, and regulatory sites will be necessary and useful to develop more appropriate approaches in the pharmaceutical development process.