The PhD Research Program (PhD by Research) is one of the greatest levels in higher education, leading to the award of a specialized research doctorate degree (PhD by Research). This program is a coordinated set of research and educational activities aimed at training specialists who, by familiarizing themselves with advanced research methods and accessing the latest research foundations, can take steps towards sustainable development, expanding the boundaries of knowledge, and enhancing the scientific level of universities and research centers in the country.

The main focus of the program is to acquire knowledge and skills through targeted research and innovation in a specific topic. Education serves to address the educational shortcomings of students in this program, facilitating the achievement of the program's objectives.

The program consists of two stages: Master of Philosophy (M.Phil) and PhD by Research. The M.Phil program lasts for one year, while the specialized doctorate lasts for three years, although the duration of both programs can be extended by the Graduate Studies Council in necessary cases to one and two academic semesters, respectively. The program is conducted in equipped research centers of Avicenna Research Institute (ARI) that have received the necessary authorization from the Council for the Expansion of Medical Universities after being evaluated by the Research and Technology Deputy of the Ministry of Health and Medical Education.

The prerequisite for registration in the call for applications is having at least two indexed articles in top-tier international databases as the first author or corresponding author, as determined by the selected committee of the Institute, as well as a language proficiency score in accordance with the standards of the Supreme Council for Planning of Medical Sciences and success in the admission interview/exam.

The total credit units for the Master of Philosophy program are determined by the advisor and based on the needs assessment conducted in relation to the student's research project by the Graduate Studies Council of the Institute. At the end of the M.Phil program, students who successfully complete the course can proceed to the next stage.

In the PhD by Research program, the student, using the skills acquired, undertakes one or more research projects aligned with the objectives of the Institute. If deemed necessary by the Institute, the student may also take specialized educational credit units related to the thesis and the field of specialization. These educational units must be completed within a maximum of six months and this period does not count towards the duration of the program. The PhD by Research concludes with the publication of research projects (at least three original research articles indexed in top-tier international databases) and the defense of the thesis.

If the student is unable to complete any of the aforementioned stages within the permitted time, ARI may refrain from issuing any form of certification (including the M.Phil certificate) to the student. According to the Ministry of Health's regulations, the responsibility for overseeing the activities of PhD students lies with the Graduate Studies Council and is based on existing laws.

Finally, the thesis and documents are evaluated by the Ministry of Health, and the graduates' academic credentials are issued based on the evaluated thesis.