As a member of the assembly, Guillotin initially directed his attention towards medical reform. As a member of the Poverty Committee, he toured the Hôtel-Dieu and contributed to the report that exposed the unsanitary conditions there. He also became first chair of the Health Committee and submitted a bill for medical reform in 1791.
The articles were fairly controversial as the rights of the criminals and their families had not previously been considered, but they were accepted over the course of several years, with the "decaptation by simple machine" one finally being accepted on 3 June 1791, with the result that his proposals became law on 20 March 1792. Meanwhile, the Assembly had commissioned Antoine Louis to build such a device. His proposal was presented on 17 March, and the first executions using it took place on 25 April 1792. However, by October 1791, Guillotin had already retired from the Assembly, returning to practise medicine. During the Reign of Terror, he moved to Arras to become the director of the military hospital there, returning to Paris a year later.