A functional neuroimaging study examined the long-term neural correlates of early adverse rearing conditions in humans as they relate to socio-emotional development. Previously institutionalized (PI) children and a same-aged comparison group were scanned using functional magnetic resonance imaging (fMRI) while performing an Emotional Face Go/Nogo task. PI children showed heightened activity of the amygdala, a region that supports emotional learning and reactivity to emotional stimuli, and corresponding decreases in cortical regions that support perceptual and cognitive functions. Amygdala activity was associated with decreased eye-contact as measured by eye-tracking methods and during a live dyadic interaction. The association between early rearing environment and subsequent eye-contact was mediated by amygdala activity. These data support the hypothesis that early adversity alters human brain development in a way that can persist into childhood, and they offer insight into the socio-emotional disturbances in human behavior following early adversity.