Background. Recurrent myoclonic seizures are associated with morphological changes in brain regions, engaging cortical as well as subcortical structures. The purpose of this study was to characterize the abnormalities of brain structural integrity in epilepsy patients with myoclonic seizures. Material and methods. Surface-based morphometry was applied to process the 3T brain magnetic resonance images acquired in 11 epilepsy patients (mean age ± standard deviation: 24 ± 6 years; 3 males) with myoclonic seizures and 11 healthy controls (28 ± 4 years; 6 males) and quantify the cortex thickness and subcortical volumes. Results. Patients with myoclonic seizures in contrast to healthy controls showed significant cortical thickness alterations in left postcentral, and bilateral rostral middle frontal and supramarginal cortices (p < 0.001, uncorrected). Cortical thickness correlated with patients‘ disease duration in left superior, middle and inferior temporal, and inferior parietal and right supramarginal, inferior parietal and rostral anterior cingulate cortices. Volumetric analysis of subcortical structures disclosed significantly lower (p = 0.014, p = 0.001) thalamic volumes (right 7078.5 ± 508.7 / left 7804.1 ± 737.4 mm3) in patients compared to healthy controls (right 8155.9 ± 702.1/left 9168.1 ± 1442.5 mm3). Conclusions. These findings evidence clear widespread abnormalities of brain structural integrity linked to myoclonic seizures and represent the neuroanatomical fingerprints that potentially underlie the generation of this seizure type.