Regular physical exercise is an important factor to reduce the indexes of cardiovascular and all causes morbimortality. However, there is, apparently, additional and independent benefits of the regular practice of physical exercise and the improvement of the level of aerobic condition. Heart rate (HR) is mediated primarily by the direct activity of the autonomic nervous system (ANS), specifically through the sympathetic and parasympathetic branches activities over the sinus node autorhythmicity, with predominance of the vagal activity (parasympathetic) at rest, that is progressively inhibited since the onset of the exercise. The HR behavior has been widely studied during different conditions and protocols associated to the exercise. A reduction of the cardiac vagal tone (parasympathetic function) and consequently a diminished HR variability in rest, independently of the protocol of measurement used, is related to an autonomic dysfunction, chronic-degenerative diseases and increased mortality risk. Individuals with high levels of aerobic condition have a lower resting HR, along with a larger parasympathetic activity or smaller sympathetic activity, but it is not necessarily a direct consequence of the exercise training, as long as other inherent adaptations to the aerobic conditioning can influence the resting HR. The HR response in the onset of the exercise represents the integrity of the vagus nerve, and the HR recovery on the post-exercise transient also denotes important prognostic information; by the way, individuals that have a slow HR recovery in the first minute post-exercise have increased mortality risk. In conclusion, the physiological mechanisms modulating HR during or after an exercise program are not totally clear, and further studies are needed.