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INTRODUCTION The aim of this research is to determine the changes in brain structures, both cortical and subcortical, in patients with drug-resistant juvenile myoclonic epilepsy (JME), in order to contribute to the understanding of the characteristics of the drug-resistant syndrome and to offer possible answers and hypotheses for further studies and more adequate treatments. SUBJECTS AND METHODS Observational case-control study. A convenience sample size of four cases and 16 healthy controls was defined to ensure the feasibility of the project (ratio of 4:1). The data collected for patients with drug-resistant JME came from 1.5T MRI equipment. FreeSurfer software was used to determine cortical and subcortical areas in both drug-resistant JME patients and healthy controls. RESULTS A total of 20 participants were included in the study, of whom four (20%) were drug-resistant JME patients and 16% (80%) were healthy controls. The clusters with statistically significant differences in cortical thickness are located in the precentral gyrus, superior temporal gyrus, transverse temporal gyrus, medial temporal gyrus and supramarginal gyrus, predominantly in the left hemisphere. CONCLUSIONS Structural brain changes are observed in patients with drug-resistant JME that may go undetected by the conventional processing techniques used in magnetic resonance imaging.