Despite the intense outpouring of American support for the persecuted Jews in Europe and the widespread condemnation of Nazism and its overt racism, World War II brought forth any number of demonstrations of the American public's own capacity for intolerance. Many Americans were swept up by a patriotic fervor that led them to champion legislation against German, Italian, and Japanese nationals, boycott immigrant-owned businesses, and sometimes resort to violence.

On December 8, 1941, armed National Guard troops were stationed on the Caltech campus and students were equipped with garden tools and instructed to protect the Institute. News of the attack on Pearl Harbor was everywhere and the campus was on the verge of panic. At 10:00 a.m., an emergency convocation was called by the Caltech registrar, himself a National Guard officer. At the meeting, the registrar lectured the audience on the evils of the Japanese enemy. Pauling, who had arrived late, interrupted the man mid-speech, demanding "By what authority have you called this impromptu convocation?" He proceeded to address both the registrar and the assembly, declaring the registrar's words and actions as unbecoming of a member of an institution of higher learning. In response, Pauling received a standing ovation from the students. The meeting was thus disbanded, with the embarrassed registrar retreating to his office.

In 1942 the U.S. government instituted the forced internment of more than 100,000 Japanese Americans settled along the West Coast, an act that horrified the Paulings. Ava Helen joined the local chapter of the American Civil Liberties Union, helping to create brochures and petition congressmen against the internment camps. Linus' war work and his frequent trips to Washington, D.C. made it difficult for him to engage in volunteer activities. Nevertheless, he was deeply concerned by the racial implications of Executive Order 9066 and wished to respond in some way. In order to prevent local Japanese American graduate students from being interred, Pauling launched a personal letter-writing campaign, requesting East Coast fellowships for selected students. This effort was largely unsuccessful. The Japanese had been badly stigmatized and universities were hesitant to accept students of questionable loyalty.

Frustrated by the intolerance apparent in American law and society, the Paulings felt that it was their responsibility to help those around them as best as they could. In the spring of 1945, the Paulings hired a young Japanese gardener at the behest of the ACLU. The man had joined the U.S. Army and was to ship out from Pasadena within a week but, until then, he needed work. On March 7, 1945, the Pauling's oldest son discovered graffiti on their mailbox and garage. "AMERICANS DIE BUT WE LOVE JAPS" was scrawled across the garage door. Two days later, Pauling received an anonymous letter that read, "We happen to be one of a groupe [sic] who fully intend to burn your home, tire [sic] and feather your body unless you get rid of that jap." Alarmed, Pauling contacted local law enforcement and demanded that an officer be sent to guard his family while he was out of town. After initial resistance from the local sheriff, Ava Helen contacted the ACLU, which came to the Paulings' aid and applied pressure to the Pasadena police.

No other threats of this type were ever made, but the experience was significant for the Paulings, especially Linus, who was shocked at the presence of such deep intolerance in his very own neighborhood. Pauling had learned a very powerful lesson about the effects of fear and propaganda. He had seen first hand the human capacity for injustice and, equally important, witnessed the power of a rational group of individuals to correct that injustice. World War II gave Pauling the opportunity to see the workings of American politics and society at both their best and worst, an experience that would inform much of his work for the next fifty years.