BACKGROUND: Definitive knowledge of the 24-hour cardiac autonomic activity in patients with allergic rhinitis (AR) is lacking. Thus, we aimed to evaluate heart rate variability (HRV), which is used to measure cardiac autonomic activity by 24-hour Holter monitoring in patients with AR. METHODS: We enrolled 32 patients who visited our clinic and were diagnosed with AR. The control group was selected four-fold (n = 128) by matching (age, sex, hypertension, and diabetes) in the AR group from a Holter registry in the cardiology department. The HRV results, which were measured using 24-hour Holter monitoring, were compared between the AR and control groups. RESULTS: All time-domain parameters of HRV revealed no differences between the groups. However, among the frequency domain parameters of HRV, the low-frequency to high-frequency ratio and low-frequency power in normalized units were significantly lower in the AR group. Conversely, high-frequency power in normalized units was significantly higher in the AR group. In the multiple regression analysis, AR was independently associated with sympathetic withdrawal (adjusted odds ratio = 3.393, P = 0.020) after adjusting for age, sex, hypertension, diabetes mellitus, and hyperlipidemia. CONCLUSIONS: The present findings suggest differences in cardiac autonomic activity which are related with sympathetic withdrawal in patients with AR compared with that in the normal population over 24 hours.