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Stopping an action at the very last moment is an important feature of human behavioural flexibility. Intentional inhibition has been defined as the ability to inhibit an action on the basis of an internal decision process. Without this ability, actions would be impulsive and would leave little space to correct misguided decisions. Previous research suggests that making a choice between action alternatives activates a specific “choice network” that includes the rostral cingulate zone (RCZ), the anterior insula (AI), the dorsolateral prefrontal cortex (DLPFC) and the inferior parietal lobe (IPL). The activity of this network has shown to be influenced by non-conscious (subliminal) stimuli. In this study, we tested whether the same regions are recruited by free-choices to inhibit and modulated by unconscious information as reported in the case of free-choices to act. Using functional magnetic resonance imaging (fMRI) we manipulated the degree of ‘freedom’ of the choice between acting and inhibiting an action by introducing explicit cues or leaving the participants free to choose between action alternatives. We included subliminal masked primes to test whether responses to targets were facilitated and/or obstructed by conditions of congruency and incongruency between primes and targets. Our findings confirmed higher activation of the “choice network” in free-choice trials when compared to cued choices. However subliminal priming failed to significantly influence participants' responses, in free-choice conditions.Masked primes were used to bias free and cued choices.Free-choices modulated activity within the RCZ, the AI, the DLPFC and the IPL.Masked priming was unable to significantly bias free-choices.Masked primes might not be ideal to determine the neural substrates of intentional inhibition.