Background: The pharmaceutical system plays an important role in ensuring the health of society, including providing access to medicines, ensuring the quality and safety of medicines, managing and monitoring the rational use of medicines and providing pharmaceutical services, Conflict of interest can have a negative effect on each of these roles. Methods: We used the qualitative research method and the interview tool to collect information about various models of conflict of interest. Expert people in the pharmaceutical system were selected with the Purposive sampling, and a semi-structured interview was conducted with them. After 42 interviews, the collected data reached saturation stage and qualitative analysis was used to analyze the textual data. Results: Different models of conflict of interests such as receiving gifts, secondary employment, financial and non-financial interests, conflict between economic interests and professional duties, history of activity in the pharmaceutical industry and friendly communication were identified in the field of personal conflict of interests and models such as conflict of duties, conflict of interests resulting from political and social pressures were in the field of institutional conflict of interests in different parts of the pharmaceutical system. Conclusion: Iran's pharmaceutical system is faced with instances of personal and institutional conflict of interests in various sectors. The types of personal conflict of interest are very similar to the types of personal conflict of interest in other studies, while the types of institutional conflict of interest have few similarities, which are rooted in the pharmaceutical laws and structures of different countries.