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It normally takes six years for a student to graduate from MIPT. The curriculum of the first three years consists exclusively of compulsory courses, with emphasis on mathematics, physics, and English. There are no significant curriculum differences between the departments in the first three years. A typical course load during the first and second years can be over 48 hours a week, not including homework. Classes are taught five days a week, beginning at 9:00 am or 10:30 am, and continuing until 5:00 pm, 6:30 pm, or 8:00 pm. Most subjects include a combination of lectures and seminars (problem-solving study sessions in smaller groups) or laboratory experiments. Lecture attendance is optional, while seminar and lab attendance affects grades. Andre Geim, a graduate and Nobel prize winner stated "The pressure to work and to study was so intense that it was not a rare thing for people to break and leave, and some of them ended up with everything from schizophrenia to depression to suicide."

MIPT follows a semester system. Each semester includes 15 weeks of instruction, two weeks of finals, and then three weeks of oral and written exams on the most important subjects covered in the preceding semester.

Starting with the third year, the curriculum matches each student's area of specialization, and also includes more elective courses. Most importantly, starting with the third year, students begin work at base institutes (or "base organizations," usually simply called bases). The bases are the core of the Phystech system. Most of them are research institutes, usually belonging to the Russian Academy of Sciences. At the time of enrollment, each student is assigned to a base that matches his or her interests. Starting with the third year, a student begins to commute to their base regularly, becoming essentially a part-time employee. During the last two years, a student spends 4–5 days a week at their base institute, and only one day at MIPT.

The base organization idea is somewhat similar to an internship in that students participate in "real work." However, the similarity ends there. All base organizations also have a curriculum for visiting students, and besides their work, the students are required to take those classes and pass exams. In other words, a base organization is an extension of MIPT, specializing in each particular student's area of interests.

While working at the base organization, a student prepares a thesis based on his or her research work and presents ("defends") it before the Qualification Committee consisting of both MIPT faculty and the base organization staff. Defending the thesis is a requirement for graduation.