Our objective was to critically evaluate the literature surrounding heart rate variability (HRV) in people with epilepsy and to make recommendations as to how future research could be directed to facilitate and accelerate integration into clinical practice. We reviewed relevant HRV publications including those involving human subjects with seizures. HRV has been studied in patients with epilepsy for more than 30 years and, overall, patients with epilepsy display altered interictal HRV, suggesting a shift in autonomic balance toward sympathetic dominance. This derangement appears more severe in those with temporal lobe epilepsy and drug-resistant epilepsy. Normal diurnal variation in HRV is also disturbed in at least some people with epilepsy, but this aspect has received less study. Some therapeutic interventions, including vagus nerve stimulation and antiepileptic medications, may partially normalize altered HRV, but studies in this area are sometimes contradictory. During seizures, the changes in HRV may be complex, but the general trend is toward a further increase in sympathetic overactivity. Research in HRV in people with epilepsy has been limited by inconsistent experimental protocols and studies that are often underpowered. HRV measurement has the potential to aid clinical epilepsy management in several possible ways. HRV may be useful in predicting which patients are likely to benefit from surgical interventions such as vagus nerve stimulation and focal cerebral resection. As well, HRV could eventually have utility as a biomarker of risk for sudden unexpected death in epilepsy (SUDEP). However, at present, the inconsistent measurement protocols used in research are hindering translation into clinical practice. A minimum protocol for HRV evaluation, to be used in all studies involving epilepsy patients, is necessary to eventually allow HRV to become a useful tool for clinicians. We propose a straightforward protocol, involving 5-minute measurements of root mean square of successive differences in wakefulness and light sleep.