During Empress Catherine the Great's reign (1763-1796), born as Princess Sophia Augusta Frederika of Anhalt-Zerbst-Dornburg, her predecessors' medical improvements in Russia flourished. She institutionalised healthcare even more, and Russia became increasingly self-sufficient in the field of trained medical professionals.
The Empress made significant changes in the management of medical affairs in Russia. In 1763 the Meditsinskaya Kantselyariya was transformed into the Meditsinskaya Kollegiya (Medical Collegium) with extended powers. She installed a board of directors (Collegium) with a Doctor Medicinae as one of the members. In 1764 the Meditsinskaya Kollegiya was given the right to confer the degree of Doctor Medicinae, although it rarely used this right.

Provincial medical charitable councils were created in all provinces of the Russian Empire in 1775. The boards, which were formed to supervise rural medical affairs, included representatives of all sections of society. Their functions included organising orphanages, alms-houses, hospitals and pharmacies. They fell under the supervision of the Meditsinskaya Kollegiya.

In 1786, the two acting medical schools were separated from the hospitals and converted into independent medico-surgical schools (the Bidloo school and the navy and land force hospital school in Saint Petersburg). They obtained the right to educate their own students and "lead them to the doctoral degree" together with Moscow University. Till that moment, this right belonged only to the Meditsinskaya Kollegiya. In 1798, 12 years later, the medico-surgical schools of Moscow and St. Petersburg had been renamed Imperial Medico-Surgical Academies. The Moscow Medico-Surgical Academy existed until 1804. Not only its 45 students but also all the medical instruments and the library were transferred to the Imperial Medico-Surgical Academy (now the Military Medical Academy named S.M. Kirov) in St.Petersburg.

At the end of the eighteenth century, two centres of medical science existed, the Medical Surgical Academy in St. Petersburg and the Medical Faculty of the Moscow University. This university faculty concentrated on general pathology, therapy and physiology, while the Medico-Surgical Academy took a leading position in the development of anatomy, topographic anatomy and surgery.
In Russia, around 1800, there was a significant gap between the medically trained scientists using experimental methods of research and the practicing physicians. The latter still relied on traditional medicine.

In the seventeenth and eighteenth centuries, close ties were established between Russia and the Netherlands in the field of medicine. Many Dutch physicians came to work in Russia, held very high positions in the Russian medical service and contributed to the development of medical services and medical education.

In particular, Leiden University has made an outstanding contribution to the development of medicine in Russia. Only six doctors of medicine were members of the Academy of Sciences, seven were professors of medical sciences, and more than thirty were simply doctors of medicine. All of them, at some point in their careers, graduated from Leiden University or received a doctorate.

It took Russia approximately 130 years to build up self-sufficient medical training since Peter the Great started reforms in Russia. By the beginning of the 19th century, Russia had already 1519 doctors and barber-surgeons of Russian origin. Four hundred twenty-two were in the army, 128 in the navy and 879 in hospitals and medical boards.

The Tsars, Emperors and Empresses have laid the foundations and created the conditions for healthcare reform from Peter the Great on. However, the doctors had to shape the house and its contents. Above all, it also asked for indispensable chief supervisors with a well-trained medical knowledge.

Both brothers, Alexander I and Nicholas I, wanted to become more and more independent from foreign medical doctors. As a great European power, they understood that Russia could not afford to fall far behind Europe after the Napoleonic War in 1812. Emperor Nicholas I (reigned 1825-1855) gave talented students from various departments of Russian universities the opportunity to study abroad. Young people, pre-selected by the professors of their universities, had to pass an entrance exam. Those who successfully passed it went to study at the Imperial German-Baltic University of Dorpat (now Tartu University in Estonia), the scholarship was awarded by the emperor. In Dorpat, students received a doctorate. Dorpat University was considered at that time one of the best higher education institutions in the German-speaking region in Europe and in Russia. The aim of their study in Dorpat and their traineeship of two more years at foreign universities in Europe was to prepare them as staff members in the Department of the Ministry of Public Education and as professors of the Universities. The first group of talented students arrived in 1828 in Dorpat, including Nikolay Ivanovich Pirogov (1810-1881). Another 30 year were needed to raise the medical skills in Russia to a level equal to that of the advanced countries of Europe, in which Pirogov played a crucial role.