Part of the revision of the Pharmaceutical Affairs Law in 2002 included the establishment of a system for independent clinical trials. According to the partial revision of the Guideline for Good Clinical Practice (GCP), MHLW Ministerial Ordinance No. 106 dated June 12, 2003, independent clinical trials are now recognized in Japan. MHLW promotes to resolve the issues about compliance with good clinical practice (GCP) guideline and the management of the clinical trials, including independent clinical trials. For our nation, more effective and safer new drug applications based on domestic independent clinical trial documents will soon be reviewed by the Pharmaceuticals and Medical Devices Agency (PMDA). For the protection of human rights, important issues about quality control and quality assurance raised by GCP Audit consist of both GCP on-site review and Document-based Conformity Review by the Office of Conformity Audit of the PMDA are studied. ^††This is not an official PMDA guidance or policy statement.