Beat-to-beat changes in cardiac signals or heart rate variability (HRV) are controlled by the two branches of autonomic nervous system (ANS) in a very complex manner. Although traditional HRV (tHRV) analysis has shown to provide information on cardiac ANS control, it often fails to isolate the effect of two branches in HRV signals. This problem becomes more obvious especially at low respiratory rates since parasympathetic activity shifts into lower frequencies and overlaps the frequency interval where sympathetic region is defined. To investigate the effect of respiration in HRV analysis we have analyzed the data of 17 healthy subjects while they were performing normal breathing (NB) and deep breathing (DB). Data were analyzed and compared using both tHRV analysis and enhanced HRV (eHRV) analysis where we used respiration to locate the frequency interval of parasympathetic activity in HRV signal. eHRV analysis provided proper isolation and more accurate detection of parasympathetic and sympathetic control of the heart.