Expanded use of exercise heart rate recovery (HRR) has renewed interest in the pathophysiology of heart rate control. This study uses basic physiologic principles to construct a unique model capable of describing the full time course of sympathetic and parasympathetic activity during HRR. The model is tested in a new study of 22 diverse subjects undergoing both maximal and submaximal treadmill exercise. Based on this analysis, prolongation of HRR involves changes within the sinus node, changes in sympathetic function, in parasympathetic function, and in the central mechanisms regulating autonomic balance. The methods may provide unique insight into alterations in autonomic control in health and disease.