A new method to evaluate endothelial function, namely, reactive hyperemia peripheral arterial tonometry (RH-PAT), has been developed. RH-PAT is an index of endothelial function, indicating initial atherosclerotic lesions. The present study aimed to investigate the effect of lifestyle modification with a focus on exercise training on RH-PAT in obese patients. We studied 43 obese patients (body mass index≧30). RH-PAT was measured, and the RH-PAT index was calculated as a ratio of the digital pulse volume during reactive hyperemia divided by that at baseline. Further, we assessed body composition, arterial stiffness, insulin resistance, adipocytokine levels, and exercise tolerance. The exercise program consisted of 30min on a cycle ergometer or treadmill, 3 times per week for 6 months. Training intensity was adjusted to the anaerobic threshold. Significant improvements were observed in the RH-PAT index following exercise training. We noted a significant reduction in weight, body fat percentage, and leptin values, and a significant increase in adiponectin levels and exercise tolerance. An abnormal baseline RH-PAT index was observed in 24 patients (55.8%); however, the improvement rate was higher in these patients than in patients with normal RH-PAT index values. Stepwise multiple regression analysis revealed that changes in insulin resistance (ΔHOMA-IR) were independently correlated with changes in the RH-PAT index. Our results indicate that lifestyle modification with a focus on exercise training improved the RH-PAT index in obese patients. Patients with abnormal RH-PAT index values before lifestyle modification with exercise training demonstrated a high rate of improvement following exercise. Further, our results suggest that insulin resistance was the only independent factor influencing improvement in endothelial function.