Developmental disabilities (e.g. attention deficit disorder; cerebral palsy) are frequently associated with deviations of the typical pattern of motor skill maturation. Neurophysiologic tools, such as transcranial magnetic stimulation (TMS), which probe motor cortex function, can potentially provide insights into both typical neuromotor maturation and the mechanisms underlying the motor skill deficits in children with developmental disabilities. These insights may set the stage for finding effective interventions for these disorders. We review the literature pertaining to the use of TMS in pediatrics. Most TMS-evoked parameters show age-related changes in typically developing children and some of these are abnormal in a number of childhood-onset neurological disorders. Although no TMS-evoked parameters are diagnostic for any disorder, changes in certain parameters appear to reflect disease burden or may provide a measure of treatment-related improvement. Furthermore, TMS may be especially useful when combined with other neurophysiologic modalities (e.g. fMRI). However, much work remains to be done to determine if TMS-evoked parameters can be used as valid and reliable biomarkers for disease burden, the natural history of neurological injury and repair, and the efficacy of pharmacological and rehabilitation interventions.