Following the war, Pauling returned to his own research. He launched himself into a study of the structure of DNA, developed a theory of molecular disease, and began a course of research on proteins. In 1954 he was awarded the Nobel Prize for Chemistry for "research into the nature of the chemical bond and its application to the elucidation of complex substances." In some ways, it was as if the war had only registered as a brief interruption from normal routine for Pauling.

But in reality the war had changed him. In his own laboratory, with his own work, he had seen how science could improve and even save lives. In the newspapers and radio reports, though, he had seen just how much pain and suffering could come from scientific pursuits. As with so many others, the atomic bomb had changed his understanding of the world.

Following the bombings of Hiroshima and Nagasaki, Pauling began an in-depth study of collected research on nuclear energy. With his extensive chemistry knowledge and background in quantum mechanics, the mechanics of nuclear weaponry quickly became clear to him. He began giving public talks on atomic weapons, explaining the bomb in simple terms to non-scientists. He also began to take note of those fellow scientists who spoke out against nuclear weapons. Not long after the atomic attacks in Japan, he declared "I feel that, in addition to our professional activities in the nuclear field, we should make our voices known with respect to the political significance of science."

The second World War had convinced him that humanity could not survive another full-scale war in which nuclear weapons were used. Alarmed by the new world order that U.S. technology had created, he launched an extensive campaign to end nuclear proliferation. Throughout the post-war and Cold War era, he lectured and petitioned, working to unite scientists and academics against nuclear weapons. In 1963 following a partial test ban treaty signed by the U.S. and USSR, Pauling was awarded the Nobel Peace Prize, making him the only individual in history to win two unshared Nobel Prizes.

Until his death in 1994, Pauling was one of the most public scientists and activists in the United States. His work in the laboratory revolutionized modern chemistry and biology, and his political activism spearheaded a major peace movement among scientists and intellectuals around the world.

Despite his dedication to the peace movement, Pauling remained proud of his contributions to the war effort. During and following the war, Pauling was repeatedly honored for the contributions that he made to the Allied cause. His work was recognized by the War Manpower Commission, the NDRC and OSRD, the War Department, and the United States Navy Bureau of Ordnance. Most impressive, however, was his 1948 reception of the Presidential Medal of Merit, the highest possible honor awarded to a civilian in the United States.

It is clear that, even after throwing himself into his peace work, Pauling felt that he had served his country well for a just cause. In a 1968 interview, he was asked if he would again provide his services to the United States military if so requested. "Well, I assume that I would," he replied. "I find it hard to believe that a situation would arise where I would behave in what would be called an unpatriotic manner."