Magnetoencephalography (MEG) is a noninvasive neuroimaging tool that is increasingly becoming useful for presurgical delineation of epileptogenic zones and eloquent cortex in both lesional and non-lesional pediatric cases. During the past 10 yrs, the use of MEG in pediatric epilepsy research has increased. This paper starts with a review of the use of MEG in pediatric epilepsy. We then describe the protocol used for epilepsy patients at the pediatric MEG facility in Boston Children’s Hospital and present two case studies of intractable epilepsy obtained in our laboratory -cortical dysplasia and tuberous sclerosis complex -to illustrate our methodology in localizing epileptiform generators. In both cases, we are able to localize generators of interictal spikes in the irritative zone just outside the lesion. We also present results on localization of the somatosensory cortex based on our pediatric MEG system to illustrate the utility of MEG for identification of the eloquent cortex. We complete this review by considering advantages and limitations of MEG in children with epilepsy, its future developments and research applications. Application of MEG in pediatric epilepsy will accelerate during the coming years as different types of pediatric whole-head MEG systems and more advanced data analysis methods become available to the researchers and clinicians. These advances will lead to greater use of MEG as a complement to clinical electroencephalography, with improved noninvasive delineation of the epileptogenic zone.