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Introduction: Atherosclerotic carotid intimamedia thickness (CIMT) may be associated with alterations in the autonomic functions. The aim of this study was to investigate the effect of 6-month yoga intervention on heart rate variability (HRV) and CIMT in elderly subjects and the correlation between HRV and CIMT. Methodology: This was a randomized controlled study, in which a total of 250 subjects were enrolled. Randomization and allocation in yoga and control groups were performed using computer-generated random numbers. The CIMT was determined by B-mode ultrasonography, and cardiac autonomic function was determined through frequency domain parameter of HRV measures at baseline and after 6 months of yoga intervention. Results: Participants had a mean age of 45.4 ± 6.4 years, and a mean CIMT in control (0.70 ± 0.05) and study group (0.69 ± 0.073), and low frequency/high frequency (LF/HF) ratio in control (2.20 ± 1.05) and study group (0.57 ± 0.54). Yoga group had evidence of increased vagal activity in the frequency domain (HF and LF/HF ratio, P < 0.001) with respect to control group. Moreover, a study group showed lower intimamedia thickness (IMT) than control subjects (P < 0.01). In the whole population, LF/HF ratio positively and significantly correlated (r = 0.665, P < 0.01) to IMT. Conclusion: This study demonstrated that, after yoga intervention, LF/HF ratio is positively correlated with CIMT, a putative index of atherosclerosis, confirming cardiac autonomic neuropathy as a part of the pathophysiological pathway for atherosclerosis. It confirms that the regular yoga represents a valuable strategy to counter impairments of cardiac autonomic activity and artery structural changes.