The clinical, social and financial burden of autism spectrum disorder (ASD) is staggering. We urgently need valid and reliable biomarkers for diagnosis and effective treatments targeting the often debilitating symptoms. Transcranial magnetic stimulation (TMS) is beginning to be used by a number of centers worldwide and may represent a novel technique with both diagnostic and therapeutic potential. Here we critically review the current scientific evidence for the use of TMS in ASD. Though preliminary data suggests promise, there is simply not enough evidence yet to conclusively support the clinical widespread use of TMS in ASD, neither diagnostically nor therapeutically. Carefully designed and properly controlled clinical trials are warranted to evaluate the true potential of TMS in ASD.