Obesity is associated with low-grade systemic inflammation, in part because of secretion of proinflammatory cytokines, resulting into peripheral insulin resistance (IR). Increased oxidative stress is proposed to link adiposity and chronic inflammation. The effects of endurance exercise in modulating these outcomes in insulin-resistant obese adults remain unclear. We investigated the effect of endurance exercise on markers of oxidative damage (4-hydroxy-2-nonenal (4-HNE), protein carbonyls (PCs)) and antioxidant enzymes (superoxide dismutase (SOD), catalase) in skeletal muscle; urinary markers of oxidative stress (8-hydroxy-2-deoxyguanosine (8-OHdG), 8-isoprostane); and plasma cytokines (C-reactive protein (CRP), interleukin-6 (IL-6), leptin, adiponectin). Age- and fitness-matched sedentary obese and lean men (n=9 per group) underwent 3 months of moderate-intensity endurance cycling training with a vastus lateralis biopsy, 24-h urine sample and venous blood samples taken before and after the intervention. Obese subjects had increased levels of oxidative damage: 4-HNE (+37%; P0.03) and PC (+63%; P0.02); evidence of increased adaptive response to oxidative stress because of elevated levels of copper/zinc SOD (Cu/ZnSOD) protein content (+84%; P0.01); increased markers of inflammation: CRP (+737%; P0.0001) and IL-6 (+85%; P0.03), and these correlated with increased markers of obesity; and increased leptin (+262%; P0.0001) with lower adiponectin (-27%; P0.01) levels vs lean controls. Training reduced 4-HNE (-10%; P0.04), PC (-21%; P0.05), 8-isoprostane (-26%; P0.02) and leptin levels (-33%; P0.01); had a tendency to decrease IL-6 levels (-21%; P=0.07) and IR (-17%; P=0.10); and increased manganese SOD (MnSOD) levels (+47%; P0.01). Endurance exercise reduced skeletal muscle-specific and systemic oxidative damage while improving IR and cytokine profile associated with obesity, independent of weight loss. Hence, exercise is a useful therapeutic modality to reduce risk factors associated with the pathogenesis of IR in obesity.