Most candidate genes and genetic abnormalities linked to autism spectrum disorders (ASD) are thought to play a role in developmental and experience‐dependent plasticity. As a possible index of plasticity, we assessed the modulation of motor corticospinal excitability in individuals with Asperger’s syndrome (AS) using transcranial magnetic stimulation (TMS). We measured the modulatory effects of theta‐burst stimulation (TBS) on motor evoked potentials (MEPs) induced by single‐pulse TMS in individuals with AS as compared with age‐, gender‐ and IQ‐matched neurotypical controls. The effect of TBS lasted significantly longer in the AS group. The duration of the TBS‐induced modulation alone enabled the reliable classification of a second study cohort of subjects as AS or neurotypical. The alteration in the modulation of corticospinal excitability in AS is thought to reflect aberrant mechanisms of plasticity, and might provide a valuable future diagnostic biomarker for the disease and ultimately offer a target for novel therapeutic interventions.