The guideline for Good Clinical Practice (GCP) of new drugs was enforced as Ministerial Ordinance No. 28, dated March 27, by the Ministry of Health, Labor and Welfare. In Article 21 of the guideline, a sponsor shall prepare the operating procedures of monitoring, and perform monitoring in conformity with the procedures. The Pharmaceuticals and Medical Devices Agency (PMDA) performs the GCP review of the application of pharmaceuticals and medical devices, including both the document-based conformity review and on-site GCP review, in order to protect human subjects and ensure the integrity of data in clinical trials. The purpose of monitoring is to perform clinical trials ethically and scientifically. Important issues in monitoring raised by the GCP reviews by the PMDA are summarized in this study. Our findings both directly and indirectly reflect the verification of the GCP guidance of investigational sites. We hope that the appropriate monitoring will encourage investigators to perform clinical trials effectively, resulting in clinical trials conforming to the GCP guidelines. Our review will lead to more effective and safer new drugs and medical devices applied in Japan. This is not an official PMDA guidance or policy statement.