Methods for determining whether the brain activity of a human subject in response to a stimulus of interest or question of interest is characteristic of a state of interest, such as a deceptive state or a truthful state, are disclosed. Some methods include the use of control questions, including truthful control questions and deceptive control questions, to provide bases for comparison for responses to stimuli of interest or questions of interest. Some methods include the use of differences between two states, such as a deceptive state and a truthful state. In some methods, brain maps are generated and compared. Also disclosed are systems for detecting deception by measuring brain activity.