Introduction. Juvenile idiopathic arthritis (JIA) is a persistent type of arthritis with no defined cause that starts before the age of 16 years and lasts for at least 6 weeks. The objective of the study was to determine the indices of heart rate variability depending on the activity and duration of JIA, as well as the administered treatment. Material and methods. The study included 90 children with JIA. The number of painful and swollen joints was determined, and the global evaluation of the disease by the doctor (GEDD) and by the patient (GEDP) and the Childhood Health Assessment Questionnaire (CHAQ) were used. Paraclinical tests included a complete blood count, markers of inflammation and Disease Activity Score 28 (DAS28). Imaging examinations, such as standard 12-lead resting electrocardiography (ECG), cardiointervalography (CIG), and 24-hour Holter ECG, with the assessment of heart rate variability indices (PNN50, SDNN, SDANN, rMSSD), were performed. CIG was performed in 20 children from the experimental group. A 24-hour Holter ECG was performed in 45 children from the experimental group. Results. The mean values of PNN50, SDANN, SDNN and rMSSD in children with DAS28 < 5.1 were higher compared to children with DAS28>5.1. The mean value of PNN50, SDANN, SDNN and rMSSD was without any statistical differences in children with disease duration of more than 24 months and of less than 24 months (p>0.05). Statistically significant differences were observed in the heart rate variability (HRV) in children on glucocorticosteroids. A considerable decrease in HRV parameters was reported in patients receiving methotrexate (MTX) compared to patients not receiving MTX (p<0.001). Conclusions. CIG revealed sympathotonia more frequently than eutonia. Hypersympathetic autonomic reactivity was found more frequently. The decrease in HRV indices was due to the disease duration and disease activity, as well as glucocorticosteroids and MTX.