Initially governed according to "The Imperial Decree on the Establishment of Moscow University", in 1804 Moscow University was granted a Charter and thus considerable independence. According to the Charter the Rector and Deans of the faculties were elected by the professors; the first Rector-elect became H.A.Chebotarev, Professor of History and Philology. The University governing body was the Board of Professors; they also awarded degrees. The publications approved by the Board and printed by the University publishing house were exempt from censorship. There were four divisions within Moscow University in the early XIX century: the Department of Moral and Political Science, the Department of Physics and Mathematics, the Department of Medicine, the Department of Philology. The course of university education took three years, after final examinations the best graduates were awarded Candidate's degrees. According to the 1804 Charter the University had control over curricula and school policies in the secondary and elementary schools of the central provinces of Russia, which contributed to continuity in the programs of educational institutions at all levels.
The invasion of the French Army led by Napoleon caused a wave of patriotism in University students, many of them joined the volunteer corps in 1812. M.I.Kutuzov, who led the Russian Army, specially mentioned selfless work of the University medical professors and students.
The University buildings were burned down during the French occupation; the library, the archives, the museum and all the equipment were destroyed. After the war it was the joint effort of all educated people in Russia that made the restoration of the University possible: books, ancient manuscripts, all kinds of collections, equipment and financial aid came from research laboratories and scientists, there were donations from private citizens too. Thus 7,500 books had been collected for the University library by 1815. In spite of the difficult conditions, the academic year at Moscow University started on 1 September, 1813; in 1820s the total number of students exceeded 500.
In the early XIX century Moscow University attracted free-thinking people; student groups lead by the Kritsky Brothers, N.P.Sungurov, V.G.Belinsky, A.I.Gertsen, N.P.Ogaryov, N.V. Stankevitch were well known. They united the young people who discussed the future of Russia. It was often a real battle of wits between the supporters of Western ideas and those who thought Russia had its own unique way of development. In 1840s public lectures, delivered by T.N.Granovsky, were attended by all Moscow intellectuals. Moscow University was a melting pot, where young people form the various strata of the society met and overcame their social prejudices; it was at the University that the traditions of fraternity were supported and cultivated. University alumni took the most advanced ideas with them when they left their alma mater.
The work of the University publishers was not limited to only scientific papers; they were the first to publish "Sonnets" by A.Mitskevich and I.C.Turgenev's prose.
Abolishing serfdom in Russia in 1861 was a turning point in the history of the country. In the history of Moscow University a period of reforms started too. The 1863 University Charter set new standards and requirements: the demand for highly qualified specialists in the field of industry, agriculture, commerce was growing; the country needed well-educated government officials, lawyers and military men. The new Charter widened the range of the subjects in the curriculum, which included more seminars and laboratory experiments. The number of professors and instructors increased, and the tradition of electing the Rector and Deans that had been discontinued for some time was re-established. There were four divisions within the University: the Faculty of History and Philology, the Faculty of Physics and Mathematics, the Law Faculty, the Faculty of Medicine. The total number of students was about 1500, most of them commoners.