Five cities were proposed as targets: Kyoto, Hiroshima, Yokohama, Kokura and Niigata. The armed forces were instructed to exclude these cities from conventional firebombing: the project director, General Leslie Groves of the US Army Corps of Engineers, and his team of scientists wanted a 'clean’ background so the effect of the bomb could be easily assessed. They also wanted visual targeting without cloud cover so damage could be photographed.

Henry Stimson, the US Secretary of War, was concerned that America’s reputation for fair play might be damaged by targeting urban areas. General George Marshall had a similar view, believing the bomb should be used first on military targets and only later on large manufacturing areas after first warning the surrounding population to leave. Both men’s views were ignored.