The involvement of autonomic imbalance has been reported in the pathogenesis of hypersensitivity reactions. Allergic diseases are more frequent in children and some of predisposing factors may be changed according to the increasing age, but the involvement of autonomic imbalance has not been investigated in pediatric population. In this cross-sectional, case-control study, we evaluated the autonomic system by measuring heart rate variability (HRV) in pediatric patients with allergic rhinitis. Thirty-five pediatric patients with allergic rhinitis and 36 healthy children (mean age 11 ± 2.7, and 12 ± 3 years, respectively) were enrolled in the study. Age and gender were not different between the groups. The diagnosis of allergic rhinitis was based on the history, symptoms, and skin prick tests. Participants with acute infection, nasal polyposis, bronchial asthma, and any other medical problems, assessed by history, physical examination and routine laboratory tests, were excluded. Twenty-four hour ambulatory electrocardiographic recordings were obtained, and the time domain and frequency domain indices of HRV were analyzed. We found significant increase in calculated HRV variables in children with allergic rhinitis compared to controls, which reflect parasympathetic tones, such as number of R-R intervals exceeding 50 ms, root mean square of successive differences between normal sinus R-R intervals, the percentage of difference between adjacent normal R-R intervals, and high frequency. These results indicate that HRV is increased, which implies sympathetic withdrawal and parasympathetic predominance. We propose that autonomic imbalance may be involved in the pathophysiology of allergic rhinitis in pediatric patients.