Recent data suggest that subthreshold presentation of emotional information is relayed to the amygdala along subcortical pathways. We examined the effect of backward masked neutral and anxious faces on the social decisions of a group of high functioning children with autism ages 7-13 years and matched controls. Participants were asked to select the friendliest of two faces, one of which was associated with the subthreshold (33 ms) presentation of an anxious face (A/N) and the other a subthreshold neutral face (N/N). Neutral paired faces were selected more often than A/N paired faces by both groups. However, children with autism selected significantly fewer N/N stimuli and more A/N stimuli than controls. These results suggest that the social choices of children with autism were influenced less by emotional information presented subconsciously and suggest a subcortical contribution to the social/emotional processing deficits observed in autism.