Studies show that yogic type of breathing exercises reduces the spontaneous respiratory rate. However, there are no conclusive studies on the effects of breathing exercise on heart rate variability. We investigated the effects of non-yogic breathing exercise on respiratory rate and heart rate variability. Healthy subjects (21-33 years, both genders) were randomized into the intervention group (n=18), which performed daily deep breathing exercise at 6 breaths/min (0.1 Hz) for one month, and a control group (n=18) which did not perform any breathing exercise. Baseline respiratory rate and short-term heart rate variability indices were assessed in both groups. Reassessment was done after one month and the change in the parameters from baseline was computed for each group. Comparison of the absolute changes [median (inter-quartile ranges)] of the parameters between the intervention and control group showed a significant difference in the spontaneous respiratory rate [intervention group -2.50 (-4.00, -1.00), control group 0.00 (-1.00, 1.00), cycles/min, P<0.001], mean arterial pressure [intervention group -0.67 (-6.67, 1.33), control group 0.67 (0.00, 6.67), mmHg, (P<0.05)], high frequency power [intervention group 278.50 (17.00, 496.00), control group -1.00 (-341.00, 196.00), ms2 P<0.05] and sum of low and high frequency powers [intervention group 512.00 (-73.00, 999.00), control group 51.00 (-449.00, 324.00), ms2, P<0.05]. Neither the mean of the RR intervals nor the parameters reflecting sympatho-vagal balance were significantly different across the groups. In conclusion, the changes produced by simple deep slow breathing exercise in the respiratory rate and cardiac autonomic modulation of the intervention group were significant, when compared to the changes in the control group. Thus practice of deep slow breathing exercise improves heart rate variability in healthy subjects, without altering their cardiac autonomic balance. These findings have implications in the use of deep breathing exercises to improve cardiac autonomic control in subjects known to have reduced heart rate variability.