CONTEXT: Resting heart rate variability (HRV) is a measure of the modulation of autonomic nervous system (ANS) at rest. Increased HRV achieved by the exercise is good for the cardiovascular health. However, prospective studies with comparison of the effects of yogic exercises and those of other endurance exercises like walking, running, and swimming on resting HRV are conspicuous by their absence. AIMS: Study was designed to assess and compare the effects of yogic training and swimming on resting HRV in normal healthy young volunteers. SETTINGS AND DESIGN: Study was conducted in Department of Physiology in a medical college. Study design was prospective randomized comparative trial. SUBJECTS AND METHODS: One hundred sedentary volunteers were randomly ascribed to either yoga or swimming group. Baseline recordings of digital electrocardiogram were done for all the subjects in cohorts of 10. After yoga training and swimming for 12 weeks, evaluation for resting HRV was done again. STATISTICAL ANALYSIS USED: Percentage change for each parameter with yoga and swimming was compared using unpaired t-test for data with normal distribution and using Mann-Whitney U test for data without normal distribution. RESULTS: Most of the HRV parameters improved statistically significantly by both modalities of exercise. However, some of the HRV parameters showed statistically better improvement with yoga as compared to swimming. CONCLUSION: Practicing yoga seems to be the mode of exercise with better improvement in autonomic functions as suggested by resting HRV.