How do people decide what actions are or are not immoral? One theory suggests that the psychological process of moral judgments revolves around the perceived harm that is done by a given agent, however past tests of this idea rely upon self-reports. Here we provide a critical test of this perspective with functional brain imaging, recruiting a diverse community sample of 35 healthy men who each completed 100 judgments (3500 total) of diverse scenarios, including whether they were immoral, harmful, unpleasant, gross, intentional, and weird, while undergoing functional magnetic resonance imaging (fMRI). Mean levels of whole-brain activity during immorality and harm judgments did not statistically differ. Further, the pattern of activity in a neural ‘morality network’ during immorality judgments was more similar to the pattern of activity during harm judgments (versus other judgment-types). These neural findings suggest that judgements of immorality are, at their heart, determinations of intentional harm-doing.