In the summer of 1941, Harald Sverdrup, the Norwegian-born Director of the Scripps Institution of Oceanography (SIO) in La Jolla, California, was denied security clearance to work on Navy-sponsored research in underwater acoustics applied to anti-submarine warfare. The clearance denial embarrassed the world renown oceanographer and Arctic explorer, who repeatedly offered his services to the U.S. government only to see scientists of far lesser reputation called upon to aid the war effort. The official story of Sverdrup's denial was the risk (...) of blackmail over relatives in occupied Norway. Declassified documents tell a different story. Although Sverdrup's integrity was defended on the highest levels of U.S. science, doubt was cast upon him by members of his own institution, who accused him of being a Nazi sympathiser. Personal distrust, rooted in scientific and intellectual disagreement, spilled over into questions about Sverdrup's loyalty and judgement. These doubts were considered sufficient grounds for withholding clearance, until Roger Revelle, a former student of Sverdrup now working within the Navy, was able to obtain a limited clearance for Sverdrup to develop techniques to forecast surf conditions during amphibious assaults. After the war, this work was credited with saving many lives, but at the time it placed Sverdrup out of the mainstream of Navy-sponsored oceanographic research. In being denied access to major areas of scientific work, Sverdrup's position as a leader of American oceanography was undermined.The loyalty case of Harald Sverdrup illustrates the emergence of an institutional apparatus through which the U.S. military began to control and shape the organisation of American science in the twentieth century. Military sponsorship of scientific research, begun during the open conflicts of World War II and continuing into the simmering tensions of the Cold War, involved explicit control by the U.S. military of who had access to critical information. This in turn meant who could do science in conjunction with the military. As the U.S. Navy became the principal sponsor of oceanography in the post-war years, clearance to do military work became to a great extent clearance to do oceanography. Choices about who could be trusted were also choices about who would do science, and what kind of science they would do. (shrink)