This study focuses on researching of heart rate variability (HRV) in rats with autoimmune myocarditis. Intact rats were investigated additionally. It was registered 2-, 5- and 20-min duration ECG from awake animals at rest-conditions and after cooling probe (CP), and then time domain and spectral parameters of HRV were calculated. We shown that 1) after CP decreasing of parasympathetic influence and augmentation of sympathetic influence on heart rate regulation in rats with autoimmune myocarditis was more manifested than in intact rats, 2) in CP with the 5-min ECG interval\'s duration was more informative for HRV estimation, 3) intracardiac inflammation leads to modification of correlation interconnection between some HRV-parameters, and that may talk about features of heart\'s chronotropic regulation in rats with autoimmune myocarditis.