Background: Presentation of epileptic seizures throughout the day is a non-random phenomenon that is strongly dependent on neural synchronization of locally and distantly interconnected cortical and/or subcortical networks. Here we aimed to identify the structural correlates that underlie the propensity of seizures to occur during the night- and daytime. Material and methods: We performed brain magnetic resonance imaging (MRI) at a 3Tesla scanner in 13 patients (28 ± 9 years) with nocturnal seizures, in 12 patients (26 ± 9 years) with diurnal seizures and in 10 healthy controls (28 ± 4 years) in order to compute the cortical and subcortical volumes by using FreeSurfer processing stream. Results: Patients with nocturnal seizures showed greater volumes of bilateral insula, superior temporal and orbitofrontal cortices compared to those with diurnal seizures. When compared to healthy controls, patients with nocturnal seizures showed smaller volumes of left postcentral and right middle temporal cortices. Patients with diurnal seizures in comparison to healthy controls displayed reduced cortical volumes mainly in frontal, temporal and parietal lobe regions of the right hemisphere. Patients with nocturnal seizures showed larger volumes of hippocampus (8208.6 ± 1006.1 mm3) than patients with diurnal seizures (3859.1 ± 508.1 mm3, p = 0.02) as well as larger volumes of amygdala (1797.3 ± 323.2 mm3 vs 1500.5 ± 246.2 mm3, p = 0.03). Conclusions: Epileptic seizures in patients with nocturnal seizures and diurnal seizures are related to distinct neuromorphological correlates that could be regarded as potential substrates favoring the generation of seizures during the night- or daytime.