PURPOSE: Heart rate variability (HRV) reflects the balance between the functional outputs of the sympathetic and parasympathetic nervous systems. It is lower in patients with epilepsy than in the healthy controls. However, HRV has been inadequately studied in different patient subgroups with medically controlled epilepsy. Hence, this study aimed to investigate factors associated with interictal HRV in patients with medically controlled epilepsy. METHODS: This retrospective cohort study included 54 patients (24 males and 30 females) with medically controlled focal epilepsy who only received monotherapy to eliminate the confounding effect of different antiseizure medications (ASMs). Patients with major systemic or psychiatric disorder comorbidities were excluded. For HRV analysis, electroencephalography and 5-minute well-qualified electrocardiogram segment recording were conducted during stage N1 or N2 sleep. In addition, the association between age, gender, seizure onset type, ASMs, and the time domain and frequency-domain HRV measures was analyzed. RESULTS: HRV negatively correlated with advanced age. Patients with focal to bilateral tonic-clonic seizure (FBTCS) had a significantly lower HRV than focal impaired awareness seizures (FIAS). HRV was not associated with any gender and ASMs. CONCLUSIONS: HRV negatively correlated with age, and patients with FBTCS had a decreased HRV. Thus, these patients may have a declining autonomic function. Therefore, different seizure types may carry different risks of autonomic dysfunction in patients with medically controlled focal epilepsy.