Increased concentrations of plasma homocysteine are known as a risk factor for cardiovascular disease. However, plasma homocysteine reactions to different types of training and detraining are not well specified. The aim of this study is to determine the effects of different methods of exercise training and detraining on plasma homocysteine levels and the risk factors associated with obesity in sedentary young men. This quasi-experimental study has been conducted on 39 randomly-sampled sedentary male students studying at Islamic Azad University of Zahedan, Iran, in the year 2014.Participants were randomly divided into three groups (aerobic experimental, anaerobic experimental, and control) of 13 members. Training programs were run three days a week for a period of 10 weeks and with preset duration and intensity (aerobic exercise training at 50 to 70 percent Vo2max and anaerobic exercise training at 95 to 100 percent Vo2max).The control group did not exercise at all. Blood samples were taken at three points: after 14 hours of fasting before the start of the study, 48 hours after the last training session, and after 4 weeks of detraining. Data analysis was performed using the ANOVA and the repeated measures ANOVA. Ten weeks of aerobic and anaerobic exercise training significantly decreased plasma homocysteine levels, body fat percentage, BMI and WHR(p<0.005).However, after 4 weeks of detraining, plasma homocysteine levels increased significantly(p<0.005)whereas the other variables had a non-significant increase (p<0.005). Both aerobic and anaerobic training methods are effective in reducing the threat of cardiovascular disease by reducing plasma homocysteine levels and the risk factors associated with obesity whereas detraining destroys the benefits of good exercise training.