Among a range of cognitive functions of the amygdala, recent studies suggest its involvement in identification of the pupil size. To further address its role, we investigated the response of the amygdala to human and cat faces with varied pupil size, taking into account the effect of the gender and subjective attractiveness ratings. Twenty-seven subjects underwent functional magnetic resonance imaging while viewing faces with large and small pupils. Large pupil faces induced increased activation in the amygdala, without interactions with either subject or stimuli gender, although no equivalent activation differences were seen for cat face stimuli. The activation differences were irrespective of the perceived attractiveness, and without explicit knowledge about the manipulation of the pupil size. These data support the idea that the amygdala is responsive not only to explicit or implicit fear, abhorrence or preference, but also to other elements that might suggest heightened vigilance of biologically relevant stimuli, which does not necessarily require subjective awareness.