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Guizhou Medical University was originally established in 1938 as the "National Guiyang Medical College," one of the nine higher medical colleges that were first under the Ministry of Education of the Nationalist Government. Its first president was Professor Li Zong'en, an early Chinese tropical disease expert and medical educator from Peking Union Medical College. Under his leadership, a large number of well-known domestic experts and scholars with outstanding academic achievements, such as Yang Chongrui, Zhu Zhanggeng, Tang Peisong, Jia Kui, Yang Jishi, Liu Weide, Hong Qian, Lin Shaowen, Hou Baozhang, Zhang Xiaoqian, Guo Bingkuan, Wang Jiwu, Zhu Maogen, Li Ruilin, Li Yi, and Wang Zhijun, gathered at the National Guiyang Medical College, which was known as the "Little Peking Union Medical College" at the time and pioneered higher medical education in Guizhou.
In 1950, the title "National" was dropped, and the university was renamed "Guiyang Medical College," placed under the administration of the Guizhou Provincial People's Government. In 1965, the "Department of Traditional Chinese Medicine" was separated and reorganized as "Guiyang College of Traditional Chinese Medicine" (now Guizhou University of Traditional Chinese Medicine). In 1981, it became one of the first institutions in China authorized to grant master's degrees; in 2003, it became authorized to grant doctoral degrees; and in April 2015, it was renamed "Guizhou Medical University." The university is a participant in the National Basic Capacity Building Project for Universities in Central and Western China, and is supported by Suzhou University and the Chinese Academy of Medical Sciences & Peking Union Medical College.