At Harvard Medical School, as Swan later recalled, he was part of an outstanding cohort of students, taught by "a remarkable line-up of teachers who sparked our interest and guided our activities." Though already married and a father during his medical school years, his academic achievements earned him the Henry Asbury Christian Award during his senior year, and he was the class valedictorian. After graduation, he returned to Denver for a year's fellowship in pathology at Colorado General Hospital. From 1940 to 1943, he did his internship and surgical residency at Peter Bent Brigham Hospital and the Children's Hospital in Boston. There, working with pioneering pediatric surgeons such as William E. Ladd and Robert Gross, Swan decided to specialize in this area.
Meanwhile, however, America had entered World War II, and many of Harvard's senior interns and residents had entered military service. This exodus depleted the medical staff at Children's Hospital, and Swan found himself covering several surgical services at once during the final months of his residency. He consequently got a much more extensive and varied operating experience than he would have during peacetime. In 1943, Swan himself was assigned to active military duty, as a member of the 4th Auxiliary Surgical Group, where his surgical experience would be expanded yet again.
The Auxiliary Surgical Groups were a recent innovation developed by the Surgical Consultants Division of the Army Surgeon General's office, which included Michael DeBakey. The consultants, responsible for providing the Surgeon General with recommendations concerning all aspects of providing optimal surgical care for army personnel, discovered that the Army's medical branch was seriously unprepared for the war in many areas. Their most urgent concern was ensuring excellent, immediate surgical care for seriously wounded soldiers at the field and evacuation hospitals. As they traveled to these installations in Europe and the Mediterranean, they found that well-trained surgeons were in short supply. The few board-certified surgeons trained at accredited surgery programs were available only in designated Army hospital centers far behind the lines or back in the United States. This seemed backwards to the consultants, because most of the seriously wounded could not survive evacuation to the hospital centers. DeBakey and his colleagues conceived the idea of organizing mobile surgical teams, each comprising a well-trained chief surgeon, an assistant surgeon, an anesthesiologist, a surgical nurse and two technicians. The teams--initially called Auxiliary Surgical Groups--were assembled by surgical specialty (General, Thoracic, Orthopedic, etc.) The first teams were deployed to the Fifth Army in North Africa, Sicily and Italy in 1943. The careful records these teams kept demonstrated a dramatic increase in survival expectations and more teams were assembled as the Normandy invasion plans took shape. (The surgical groups were later renamed Mobile Auxiliary Surgical Hospital (MASH) units and became well known for their service in the Korean and Vietnam conflicts.)
Swan was the assistant surgeon in "the Fourth," which shipped out to England in the spring of 1944 and landed on Normandy's Utah Beach on June 7 ("D-Day + 1.") The team often worked twelve-to-fourteen hour shifts, in grueling conditions, for weeks at a time. As he noted in the many letters he wrote to his wife during this time, Swan enjoyed the surgical challenges, but often found the combat injuries (and too-frequent deaths) heartbreaking. He was reassigned in October 1944, becoming chief surgeon of the 5th Auxiliary Surgical Group. As the surgical groups moved along with eastward advance of the Allied forces through France, Belgium, and Germany, they witnessed the many wartime hardships suffered by civilians. In the spring of 1945, Swan wrote of the horrible atrocity his unit discovered when they entered the German town of Gardelegen: just days before, Nazi forces retreating from the Soviet army had herded over 1,000 concentration camp prisoners into a barn and burned them alive. Like most of his companions, Swan was deeply affected by these experiences and struggled to make sense of them in his letters to his family.
By the war's end in August 1945, Swan had operated on over 1,400 non-transportable cases of penetrating wounds of the chest, abdomen, or major extremity, as well as less serious injuries. His patients included American troops, German prisoners of war, and assorted French, Belgian, and German civilians. Among these cases was his first end-to-end arterial repair, which succeeded in saving a soldier's foot from amputation. It was a non-standard procedure; damaged arteries were usually just tied off, and without enough blood circulation, the arm or leg might need to be amputated. But this success, combined with his extensive trauma surgery experience, stimulated Swan's interest in vascular surgery, and helped shape the direction of his post-war work.
After the war, Swan returned to Denver, planning to set up a private surgical practice. Soon, however, Ward Darley, the new dean of the University of Colorado medical school, made him a more interesting offer. Like many post-war medical school leaders, Darley was in the process of transforming his institution so that its programs and graduates could meet the higher standards of the hospital- and research-based medicine that had developed since the early twentieth century. The medical school was small and undistinguished, with no full-time clinical faculty and a curriculum that hadn't been updated since the 1920s. There was little research being done in the pre-clinical departments, and none in the clinical ones. The school had a two-year residency program with its one teaching hospital, Colorado General, but had no other affiliated hospitals available, no graduate programs, and no post-graduate courses. Swan was hired as the first full-time member of the surgical faculty in 1946. One of his first initiatives was to establish a small surgical research lab--the Halsted Experimental Laboratory--and obtain a U.S. Public Health Service grant to fund the first projects. He also chaired the clinical curriculum committee, which integrated much more hospital and outpatient clinic time into the junior and senior year plans. In surgery, as in other areas, the residency program expanded, and by 1951 Swan could report that the University of Colorado's surgical residents were routinely obtaining their board certifications. He was appointed chairman of the department of surgery in 1950, and continued to expand its staff, facilities, and programs for the next decade.
While teaching, operating, and building his department, Swan also started developing the experimental background and then the clinical applications of vascular and cardiac surgery, which would establish him as one of the foremost innovators in this nascent field.