The capacity to deceive others is a complex mental skill that requires the ability to suppress truthful information. The polygraph is widely used in countries such as the USA to detect deception. However, little is known about the effects of emotional processes (such as the fear of being found guilty despite being innocent) on the physiological responses that are used to detect lies. The aim of this study was to investigate the time course and neural correlates of untruthful behavior by analyzing electrocortical indexes in response to visually presented neutral and affective questions. Affective questions included sexual, shameful or disgusting topics. A total of 296 questions that were inherently true or false were presented to 25 subjects while ERPs were recorded from 128 scalp sites. Subjects were asked to lie on half of the questions and to answer truthfully on the remaining half. Behavioral and ERP responses indicated an increased need for executive control functions, namely working memory, inhibition and task switching processes, during deceptive responses. Deceptive responses also elicited a more negative N400 over the prefrontal areas and a smaller late positivity (LP 550–750 ms) over the prefrontal and frontal areas. However, a reduction in LP amplitude was also elicited by truthful affective responses. The failure to observe a difference in LP responses across conditions likely results from emotional interference. A swLORETA inverse solution was computed on the N400 amplitude (300–400 ms) for the dishonest – honest contrast. These results showed the activation of the superior, medial, middle and inferior frontal gyri (BA9, 11, 47) and the anterior cingulate cortex during deceptive responses. Our results conclude that the N400 amplitude is a reliable neural marker of deception.