We combined eye-tracking technology with a test of facial affect recognition and a measure of self-reported social anxiety in order to explore the aetiology of social-perceptual deficits in Asperger's syndrome (AS). Compared to controls matched for age, IQ and visual-perceptual ability, we found a group of AS adults was impaired in their recognition of fearful and sad expressions and spent significantly less time fixating the eye region of all faces. For AS subjects, but not controls, the extent of the failure to fixate the eyes predicted the degree of impairment at recognising fearful expressions. In addition, poor fear recognition and reduced fixation of the eyes were independently associated with greater levels of social anxiety in AS individuals. These findings support the hypothesis that avoidance of emotionally arousing stimuli, such as eyes, contributes to social-perceptual impairment in AS. Furthermore, our findings are consistent with theories implicating amygdala-mediated over-arousal and anxiety in the development of these social-perceptual deficits.