Multiple lines of evidence converge on the human amygdala as a core moderator of facial emotion perception. The major subregions of the human amygdala have been anatomically delineated, but the individual contribution of these subregions to facial emotion perception is unclear. Here we combined functional MRI (fMRI) with cytoarchitectonically defined maximum probabilistic maps to investigate the response characteristics of amygdala subregions in 14 subjects presented with dynamic animations of angry and happy relative to neutral facial expressions. We localized facial emotion-related signal changes in the basolateral and superficial (cortical) subregions of the left amygdala, with most robust responses observed to happy faces. Moreover, we demonstrate a differential neural response to happy faces in ventromedial prefrontal cortex, which is consistent with a hypothesized role of this brain region in positive valence processing. Furthermore, angry and happy faces both evoked temporopolar responses. Our findings extend current models of facial emotion perception in humans by suggesting an intrinsic functional differentiation within the amygdala related to the extraction of value from facial expressions.