Objective: To examine the respective contributions of changes in visceral adiposity, subcutaneous adiposity, liver fat, and cardiorespiratory fitness (CRF) to the improvements in cardiometabolic risk markers observed in response to a 3-year healthy eating/physical activity lifestyle intervention. Research Design and Methods: Ninety-four out of 144 viscerally obese but otherwise healthy men completed a 3-year lifestyle intervention. Body weight, body composition and fat distribution were assessed by anthropometry and DEXA/computed tomography. CRF, adipokines, lipoprotein-lipid profile and 75g oral glucose tolerance were assessed. Results: CRF, visceral and subcutaneous adiposity significantly improved over the 3-year intervention, with a nadir at year 1 and a partial regain at year 3. Liver fat (estimated by insulin hepatic extraction) stabilized from year 1 to year 3 whereas HOMA-IR, ISI-Matsuda index and adiponectin continued to improve. Multivariate analysis revealed that visceral adiposity and estimated liver fat reductions both contributed to the improved ISI-Matsuda index observed over 3 years (R²=0.28, p<0.001). Three-year changes in fat mass and in CRF were independently associated with changes in visceral fat (adjusted R2=0.40, p<0.001) whereas only changes in CRF were associated with changes in estimated liver fat (adjusted R²=0.18, p<0.001). Conclusions: A long-term healthy eating/physical activity intervention in men improves several cardiometabolic risk markers over the long-term (3 years) despite a partial body weight regain observed between year 1 and year 3. The improvement in CRF contributes to visceral and estimated liver fat losses over the long term which in turn explain the benefits of the lifestyle intervention on cardiometabolic risk profile.