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Although the nature of epilepsy and headache association has not been fully understood, during the past 100 years several potential mechanisms have been proposed to explain the link between these two conditions. Strong support for a shared genetic basis between headache and epilepsy comes from clinical/EEG and genetic studies on familial hemiplegic migraine, a rare monogenic subtype of migraine, where errors in the same gene may be associated with migraine in some cases and with epilepsy in others. Numerous genome-wide association studies and meta-analysis are identifying loci associated migraine and epilepsy susceptibility.The fundamentals of molecular genetics are important for clinicians to understand unprecedented insights into the pathogenesis of these disorders, and reveal promising treatment targets for future drug development.