Autonomic dysregulations were repeatedly observed in people with allergic reactions. Contradictory results of sympathetic over-activation on one hand and parasympathetic predominance on the other, were described for both atopic dermatitis and allergic rhinitis. Secondly, psychological traits of high anxiety and depression described in allergic patients are mostly associated with increased sympathetic and decreased vagal modulation. To address inconsistency in prior findings, we aim to study autonomic nervous system changes in allergic and highly anxious people via HR (heart rate) and HRV (heart rate variability) measures during stressful and relax days in day to day life. We further assess differences between allergic diagnoses and impact of acute symptom occurrence on HR and HRV. 61 subjects (26 allergic, 18 healthy high trait anxious and 17 healthy low trait anxious) took part in this study. They were repeatedly measured for HR by a portable electrocardiographic device, and assessed their subjectively experienced stress during everyday life. HRV was analyzed using time-domain, spectral and non-linear analyses. We observed increased HRV and decreased HR in allergic patients and also in healthy highly anxious subjects, when compared to controls. Both atopic dermatitis and allergic rhinitis patients exhibited parasympathetic predominance or sympathetic withdrawal, seen in increased HRV and lowered HR. Described effects of parasympathetic predominance were, however, not present during acute symptoms occurrence.