Doctoral study programme includes lectures and research component. The research component is primary, while lectures are intended to prepare student and help them with their research, and to provide them with wider view on their field. Lectures are mostly limited to the first year of the programme.

Student chooses one of the eight study modules:

1. Elementary particle physics
2. Nuclear physics
3. Astrophysics
4. Atomic, molecular and optical physics
5. Condensed matter physics
6. Biophysics
7. Medical physics
8. Geophysics

Research component starts at the very beginning of the programme and includes original research, writing and publication of scientific papers, and writing and defence of doctoral dissertation.

After enrolment, a counselor is assigned to the student. Counselor helps him and supervises student's progress until the assignment of the thesis mentor.

First year

Doctoral student enrols in mandatory courses, and after consultation with module coordinator, enrols elective courses. Elective courses can be enroled in the first (preferably) or the second year.

During the first year, student should take part in the seminar ("journal club") and must pass all mandatory courses.

Second year

By the end of the second year, student must pass the remaining elective courses (if any) and defend the topic of doctoral dissertation. During that time, research work with the mentor should already be intensive.

Third year

To enrol in the third year, all courses should be passed and topic of the doctoral dissertation should be defended. During the third year student gives the scientific colloquium (a.k.a. doctoral seminar) where results of their resarch are presented. Student then writes and defends the dissertation.