Thirsk was in the family medicine residency program at the Queen Elizabeth Hospital in Montreal when he was selected in December 1983 by the National Research Council of Canada to join the Canadian astronaut program. He began astronaut training in February 1984 and served as backup payload specialist to Marc Garneau for space shuttle mission STS-41-G, which flew October 5 to 13, 1984. He has participated in several parabolic flight experiment campaigns on board NASA's KC-135 aircraft and has been involved in various projects relating to space medicine, the International Space Station, mission planning, and education with the Canadian Space Agency. He led an international research team investigating the effect of weightlessness on the heart and blood vessels. His team designed and tested an experimental "anti-gravity suit" that may help astronauts withstand the effects of extended spaceflight on the cardiovascular system.