Heart rate variability (HRV) is a noninvasive measure of cardiac autonomic modulation. Time and frequency domain measures have primarily been examined in patients with type 2 diabetes mellitus (T2D). Not only do frequency domain HRV parameters tend to be reduced in T2D, but healthy individuals with low HRV are also more likely to develop T2D. Furthermore, patients with T2D with low HRV have an increased prevalence of complications and risk of mortality compared with those with normal autonomic function. These findings provide support for the use of HRV as a risk indicator in T2D. Exercise is considered an important component to T2D prevention and treatment strategies. To date, few studies have examined the changes in HRV with exercise in T2D. One study showed changes in resting HRV, two studies showed changes in HRV during or following acute stressors, and one study showed no changes in HRV but improvements in baroreflex sensitivity. The most pronounced changes in HRV were realized following the exercise intervention with the greatest frequency of supervised exercise sessions and with the greatest intensity and duration of exercise bouts. These findings suggest that exercise following current American College of Sports Medicine/American Diabetes Association guidelines may be important in the prevention and treatment of T2D to improve autonomic function and reduce the risk of complications and mortality.