Aim: Inactivity can adversely affect on health of lean subjects. A few findings are available about novel insulin resistance indices. The purpose of this study was to investigate effect of endurance training on novel insulin resistance indices and some of cardio metabolic risk factors in inactive lean men.Methodology: In a semi-experimental study, twenty inactive lean men were randomly placed at two groups: endurance training (n=10, 21.2±2.2 yr) and control (n=10, 21.4±2.7 yr). General characteristics of subjects, Adiponectin-Resistin (AR), homeostasis model assessment-Adiponectin (HOMA-AD) and insulin resistance index (IRAR), blood pressure, and lipid profile were assessed before and after training. Endurance training consisted of twelve weeks pedaling on ergometer cycle (3 sessions per week, intensity 60-70% of reserved heart rate, duration of each session 20-40 min). Data analyzed by paired- and independent-t tests. Statistical significance was accepted at P<0.05.Results: After the training period, HOMA-AD (P=0.043), IRAR (P=0.029), systolic blood pressure (P=0.022), diastolic blood pressure (P=0.038), and serum triglyceride (P=0.019) were reduced, while serum Resistin, AR, total cholesterol, high density lipoprotein, and low density lipoprotein did not change significantly (P>0.05).Conclusion: Decreases of HOMA-AD and IRAR indices, systolic blood pressure, diastolic blood pressure, and serum triglyceride after twelve weeks endurance training in inactive lean men indicate that endurance training can be useful for metabolic and cardiovascular health of inactive lean men via improving insulin resistance, blood pressure, and circulating levels of triglyceride.