The 1948 Presidential election, held in an atmosphere of growing anti-Communist fervor in the US, would prove one of the most important and surprising in the nation’s history. Pauling’s favorite candidate was neither the incumbent Harry Truman (whom he viewed as selling out the New Deal values of Franklin D. Roosevelt) nor Republican challenger Thomas Dewey. Instead Pauling, like many of the left wing of the Democratic Party, supported Henry Wallace, a Midwest corn breeder and farm journal publisher who had served as FDR’s vice-president during his last full term.

Wallace was a liberal’s liberal, an unrepentant New Dealer who believed in accommodation rather than confrontation with the Communists. When Wallace decided to mount a third-party challenge to Truman, the press and most Americans saw it as the action of an unrealistic idealist, one of the "post-war dream boys," as one observer called them. But Wallace’s dreams were the sort Pauling admired, and the Caltech scientist stumped for the Midwest farmer even when the polls showed Wallace to be well out of the race. On election night, Pauling was in Washington State speaking about peace and science. When he went to bed, the radio commentators were predicting a Republican victory. At two in the morning he awoke, went out to his car in the parking lot, and dialed around for the latest news. Truman, he heard, was now eking out a narrow but almost certain win. The Democrats would remain in power. Wallace’s showing was dismal; he received less than 3 percent of the popular vote. It was the end of the New Deal. Later, Pauling commented that Wallace "may have been too honest to be a successful politician."