The traditional philosophical doctrines of Consequentialism, Doing and Allowing, and Double Effect prescribe that moral judgments and decisions should be based on consequences, action (as opposed to inaction), and intention. This study uses functional magnetic resonance imaging to investigate how these three factors affect brain processes associated with moral judgments. We find the following: (1) Moral scenarios involving only a choice between consequences with different amounts of harm elicit activity in similar areas of the brain as analogous nonmoral scenarios; (2) Compared to analogous nonmoral scenarios, moral scenarios in which action and inaction result in the same amount of harm elicit more activity in areas associated with cognition (such as the dorsolateral prefrontal cortex) and less activity in areas associated with emotion (such as the orbitofrontal cortex and temporal pole); (3) Compared to analogous nonmoral scenarios, conflicts between goals of minimizing harm and of refraining from harmful action elicit more activity in areas associated with emotion (orbitofrontal cortex and temporal pole) and less activity in areas associated with cognition (including the angular gyrus and superior frontal gyrus); (4) Compared to moral scenarios involving only unintentional harm, moral scenarios involving intentional harm elicit more activity in areas associated with emotion (orbitofrontal cortex and temporal pole) and less activity in areas associated with cognition (including the angular gyrus and superior frontal gyrus). These findings suggest that different kinds of moral judgment are preferentially supported by distinguishable brain systems.