In the social neuroscience of face processing, multiple roles are attributed to amygdala: signalling of fear/threat-stimuli, of emotional expression, and general salience. The current study aimed at a direct comparison of amygdala activation attributable to these conditions by contrasting amygdala responses to matched emotional (threatening and non-threatening) and of non-emotional salient faces in a visual search paradigm using cartoon faces. Participants (21 healthy volunteers) had to detect a target face (angry, happy, blue, red, differing in the exact same features) in an array of closely matched non-target faces. Behavioural results revealed a pop-out effect for all targets compared to non-targets, indicating that they were all salient, independently of being emotional or non-emotional. While significant amygdala activation was obtained for all trials with salient faces (compared to those containing only non-target faces), no significant differences in activation emerged between emotional threatening, emotional non-threatening, and non-emotional targets. Moreover, right and left amygdala activation for target trials was found correlated to the behavioural measure of target detection. These findings provide evidence for a general role of the amygdala in signalling salience in a visual search independent of modality. Given the critical involvement of the amygdala in several neuropsychiatric disorders, the current findings may contribute to further our understanding on dysfunctional neural circuits in these disorders.