Aim: Controversy surrounds the distinction between high-functioning autism (HFA) and Asperger disorder, but motor abnormalities are associated features of both conditions. This study examined motor cortical inhibition and excitability in HFA and Asperger disorder using transcranial magnetic stimulation (TMS). Method: Participants were diagnosed by experienced clinicians strictly according to DSM-IV criteria. Participants with HFA (nine males, two females; mean age 16y 8mo, SD 4y 5mo) or Asperger disorder (11 males, three females; mean age 19y 1mo, SD 4y 2mo) and neurotypical participants (eight males, three females; mean age 19y 0mo, SD 3y 1mo) were administered a paired-pulse TMS paradigm intended to assess motor cortical inhibition and excitability. Responses to TMS were recorded by electromyography. Results: Cortical inhibition was significantly reduced in the HFA group compared with both the Asperger disorder (p less than 0.001) and neurotypical (p less than 0.001) groups, suggesting disruption of activity at gamma-aminobutyric acid A (GABAA) receptors. There was no group difference in cortical excitability. Interpretation: Cortical inhibition deficits may underlie motor dysfunction in autism, and perhaps even relate to specific clinical symptoms (e.g. repetitive behaviours). These findings provide novel evidence for a possible neurobiological dissociation between HFA and Asperger disorder based on GABAergic function.