We estimated quantitative susceptibility maps (QSM) in 19 children with histologically confirmed focal cortical dysplasia (FCD), a frequent cause of drug-resistant epilepsy. QSM allowed measurement of cortical and sub-cortical layered structure and its alteration in FCD lesions. Moreover, QSM was sensitive to abnormal deposits of calcium, zinc, and iron, which were validated using X-ray fluorescence in brain tissue specimens available following surgical treatment. QSM could provide a non-invasive biomarker of cortical tissue changes in epilepsy and could be used to determine alterations in mineral deposits in different brain disorders.