Metabolic syndrome (MetS) is a strong risk factor for Coronary Heart Disease (CHD) and type II Diabetes mellitus (DM). The aim of the present study was to determine whether yoga can regress early atherosclerosis in patients with MetS, as measured by carotid intima thickness (cIMT). 100 adult patients of MetS were randomized to yoga and control group and were followed for 1 year. 81% patients completed the study. At the end of 1 year, the yoga group showed a significant regression of cIMT (0.842 ± 0.176 to 0.808 ± 0.204, p<0.001) whereas there was no significant change in cIMT in the control group (0.831 ± 0.171 to 0.834 ± 0.131, p=NS). In addition the yoga group also showed greater reduction in Body Mass Index (BMI), Waist Circumference (WC), LDL cholesterol and Systolic Blood Pressure (SBP). On the basis of this randomized study, we conclude that practice of yoga can regress early atherosclerosis in MetS and has also beneficial effects on several metabolic parameters. The mechanisms of the improvement are not evident from the present study andneed further investigations.