Synchrotron-generated X-ray (SRX) microbeams deposit high radiation doses to submillimetric targets whilst minimizing irradiation of neighboring healthy tissue. We developed a new radiosurgical method which demonstrably transects cortical brain tissue without affecting adjacent regions. We made such image-guided SRX microtransections in the left somatosensory cortex in a rat model of generalized epilepsy using high radiation doses (820 Gy) in thin (200 μm) parallel slices of tissue. This procedure, targeting the brain volume from which seizures arose, altered the abnormal neuronal activities for at least 9 weeks, as evidenced by a decrease of seizure power and coherence between tissue slices in comparison to the contralateral cortex. The brain tissue located between transections stayed histologically normal, while the irradiated micro-slices remained devoid of myelin and neurons two months after irradiation. This pre-clinical proof of concept highlights the translational potential of non-invasive SRX transections for treating epilepsies that are not eligible for resective surgery. Surgical resections for intractable epilepsies have reached impressive success rates in recent years 1,2. However, the management of seizures arising from eloquent cortical regions remains challenging due to high rates (up to 50%) of post-operative neurological deficits 3–6. Non-resective procedures such as vagus nerve stimulation 7 , scheduled deep brain stimulation 8 or closed-loop neurostimulation 9 , did not achieve seizure freedom in most cases. Multiple Subpial Transection (MST), developed by Morrell et al. 10 , is currently the most effective surgical technique applicable to eloquent cortex. Transections made with a special surgical knife at intervals of 5 mm interrupt horizontal intracortical fibers, while preserving vertical fibers. The procedure is based upon experimental evidence indicating that epileptogenic discharges require substantial side-to-side or horizontal interaction of cortical neurons 11 , whereas major functional properties of cortical tissue rely greatly on vertical fiber connections of the columnar units 12. MST reduces synchronized discharges from the epileptic focus and limits their spread without impairing the function of the transected cortex 13. However, MST is an invasive procedure that only reaches moderate rates of seizure freedom because of the limited access to deep cortical tissue/sulci 14,15 and the risk of post-operative deficits, such as brain edema, infections, and bleeding 16. Radiosurgery is an attractive alternative to surgical MST but radio-transections are currently unachievable with conventional radiosurgical devices and/or mega-voltage machines since their lateral dose profile does not provide the required sharp dose demarcations between irradiated and non-irradiated tissue slices 17,18. Further, the transection procedure requires focused delivery of hectogray doses 19 , currently only achievable at 3 rd generation synchrotron facilities. The assessment of the efficacy of synchrotron radiation for seizure management in rodents has been studied during the last few years using different methods and irradiation configurations 20–23. The purpose of the present study was to perform a novel method of non-invasive cortical transections in epileptic rats using synchrotron x-rays (SRX) and to quantify the induced changes of normal and pathological electrical activities. To achieve