Although features of epilepsy display strong circadian variation and >80% of protein coding genes display circadian rhythmicity, the chronobiology of epilepsy remains poorly understood at the molecular level. Circadian rhythms are present in all mammalian cells and endogenously control behavioral/physiological processes over 24-hours period. They are regulated by both external factors (light/dark) and internal cues (molecular clocks). Clock genes are rhythmically expressed throughout the brain and are critical to regulate brain homeostasis and in disease. The epileptogenesis process is associated with large-scale changes in gene expression, which contribute to the remodeling of brain networks permanently altering excitability. These impactful changes are largely regulated and under strong circadian variation. Here, it will be systematically addressed the dysregulation in diurnal rhythms during epileptogenesis, providing insights into potential mechanisms that underlie changes in gene expression and rationale for pursuing the study of the molecular clock in epilepsy.