Since deception-induced mood and somatic states may vary across individuals, a marker of deception independent of anxiety or guilt is important. Regional brain activity, manifest as a blood oxygenation level dependent (BOLD) response. elicited by inhibition of the truth response during intentional deception has been demonstrated to serve as such a marker. Unlike the ERP, the spatial resolution of BOLD event-related (questioning) functional MRI neuroimaging is sufficient to anatomically localize changes in cerebral blood flow related to regional neuronal activity during cognition.

A number of publications in peer-reviewed medical journals have used MRI to identify deceptive and truthful responses. Deceptive responses were associated with increased activity in specific areas of the brain. These results indicate that cognitive differences between deception and truth have neural correlates that can be detected by fMRI.

fMRI has shown that suppression of a particular thought, when compared to free-thought control condition, revealed greater activation in certain specific areas of the brain. fMRI can distinguish the suppression of all conscious thoughts compared to free-thought. fMRI can also distinguish truth and false visual recognition. The sensory signal distinguishing truth from deception may not be accessible to conscious awareness, indicating that intentional deception can be identified.