The supreme steering body of the Association is the General Assembly, which decides about the Association’s  strategic direction. It comprises of high representatives of individual member companies, usually general directors for the Czech Republic or several Central European countries. The General Assembly elects Board members. The Board is the AIFP’s  elected executive body comprising of seven members. It meets twice a  month and decides about important steps within the strategy laid down by the General Assembly. 
AIFP Executive Team takes care of running of the Association, which is represented by an executive director Mgr. Jakub Dvořáček, MHA, LL.M. The Association is supervised by two bodies – Controlling Committee and Ethics Committee. The Audit Committee supervises the Association’s financial management, checks the minutes from General Meetings and submits recommendations to the Board. The Ethics Committee checks the compliance with the AIFP Code of Practice and other standards of the AIFP. It regularly checks non-intervention clinical trials commissioned by the AIFP’s member companies (as to whether or not all requirements were observed during these trials).    
Several Working groupsPlatforms and Task Forces comprising of the representatives of member companies meet on the AIFP’s neutral ground. Nominated professionals focus on specific areas that are somehow linked to the core goals and values of the Association.    
Complete structure of the AIFP is depicted in Organogram, that also includes Association’s projects and initiatives devoted to patients, Scientific Societies, pharmaceutical industry or general public, e.g. online advisory centre Clinical TrialsAcademy of Patient Organizations (APO), training for employees of the member companies like Certification of sales representatives or Disclosure Project