This article examines how the Kennedy administration assessed the risk posed by Soviet short-range missiles in Cuba and the associated combat troops, particularly in the months after the peak of the Cuban missile crisis. The issue had a strong domestic political subtext that played out for months. Missiles in Cuba had been a topic of discussion well before the dramatic events of October 1962, and the dispute about them dragged on well past the famous “thirteen days.” Many studies assume a final resolution to the crisis that did not actually exist. The evidence from this period indicates that domestic political considerations were a fundamental factor in Kennedy's decision-making and apparently induced him to take a slightly harder line in the post-crisis negotiations with the Soviet Union than he otherwise might have. But the evidence also suggests that Kennedy was more willing than some of his advisers and many Congressional critics to accept a degree of permanent military risk in Cuba.