Background and objectives The hospital pharmacist, in charge of the pharmaceutical aspects of clinical trials plays a central role in the management and the proper use of investigational health products (IHP), in accordance with the Good Clinical Practices and Public Health Code. The working group “Clinical trials” of the CPCHU (French University Hospitals Pharmacists’ Commission) aimed to prepare national guidelines to describe the activities and involvement of the pharmacists, whatever the type of health care institution. Methodology After an analysis of the existing literature, form and content requirements were set and the structure was established. The chapters were written in subgroups, with systematic revision and validation in plenary. Results The professional guidelines are composed of 109 pages and are available as an interactive pdf file on the SFPC and CNCR websites. Topics covered in the guidelines are divided into 4 chapters, and include inserts of specific recommendations and/or some illustrations. There are 374 references, including 329 regulatory texts, and 5 appendices. Discussion–conclusion These guidelines are a part of process of dissemination, standardization and securing practices, in order to help hospital pharmacists in the management of IHP and in the development or improvement of their own performance systems in terms of quality. Its pedagogical format also makes it a training tool for students, compounders and senior pharmacists. Its regular updating is necessary.