Current clinical practice of resective surgery in focal epilepsy involves electroencephalogram (EEG) brain source imaging to localize irritative brain areas from where Inter-ictal epileptiform discharges (IEDs) emerge, useful to localize the seizures-onset zones. Unfortunately, there are no previous systematic studies to characterize the pathophysiological mechanisms and abnormal cellular substrates in these irritative areas since histological data are available only from the final resective zones. To address this issue we applied a combination of EEG brain imaging described by Bae et al. (2015) using cutting-edge technology for high-density scalp EEG in rodents and histological analysis on a chronic rat model of focal cortical dysplasia. Post-mortem brain sections were stained for anatomical, functional and inflammatory biomarkers. Abnormal anatomical structures and increased expression of inflammatory biomarkers were found in the irritative regions. We conclude that IED-based brain source imaging can help to localize abnormal tissues highly prospective for epileptogenesis.