BACKGROUND: Specific nostril breathing is known to influence autonomic functions. AIM: The study was to assess the effects of right nostril breathing (RNB) and left nostril breathing (LNB) on heart rate variability (HRV) and cardiovascular functions. MATERIAL AND METHODS: Eighty-five student volunteers were divided into three groups: RNB group (n = 30), LNB group (n = 30), and control group (n = 25). RNB and LNB group subjects practiced right and left nostril breathing, respectively, every day 1 h for 6 weeks. The control group did not practice nostril breathing. Cardiovascular parameters and spectral indices of HRV were recorded before and after 6-week practice of nostril breathing. In RNB and LNB groups, prediction of rate-pressure product (RPP) by low-frequency to high-frequency ratio (LF-HF) of HRV was assessed by bivariate logistic regression. RESULTS: HRV indices representing sympathetic activity were increased in the RNB group and indices representing parasympathetic activity were increased in LNB group following 6-week nostril breathing. Prediction of LF-HF to RPP, the marker of cardiovascular risks, was more significant (OR 2.65, P = 0.005) in the LNB group compared to the RNB group (OR 1.452, P = 0.016). CONCLUSIONS: Short-term practice of LNB improves vagal tone, increases HRV, and promotes cardiovascular health of medical students. Practice of RNB increases sympathetic tone and could jeopardize cardiovascular health.