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Asperger syndrome (AS) is a neurobiological condition which is characterized by poor skills in social communication, and restricted and repetitive patterns of behavior and interests. We studied whether stress-related indices of heart rate variability (HRV) and electroencephalography (EEG) are different in children with AS than normal controls. We analyzed retrospectively the data of the test where audiovisual stimuli were used. We hypothesized that this test is a stressful situation for individuals with AS and they would have a greater reaction than control subjects. EEG and one-channel electrocardiography (ECG) were collected for children with diagnosis of AS (N = 20) and their age-matched controls (N = 21). HRV indices, frontal EEG asymmetry index and brain load index were calculated. HRV based indices revealed increased sympathetic activity during the test in children with AS. EEG based indices increased more in children with AS during the test compared to baseline. Thus, the children with AS seems to have a greater reaction to stressful situation.