Being confined to bed rest has negative physiological consequences. Bed rest represents a unique model of physical inactivity and results in changes in cardiovascular, neural and metabolic function. In particular, reduced skeletal muscle mitochondrial capacity and a reduction in intrinsic mitochondrial function in response to physical inactivity may have broad implications for human disease. The aim of the present study was to test the hypothesis that physical inactivity, through the model of bed rest, will decrease mitochondrial function, insulin sensitivity and muscle mass in healthy young men. A reduction in lean muscle mass was evident after bed rest (p<0.05). This was accompanied by a reduction in skeletal muscle insulin sensitivity (p<0.05). Citrate synthase as a marker of mitochondrial content was reduced after bed rest (p<0.05). O2 flux expressed per mg of wet weight of muscle tissue was lower during LEAK respiration following 21 days of BR (p<0.05). OXPHOS and ETS capacity, indicative of maximal capacity, were increased following bed rest when normalized to citrate synthase activity (p<0.05). Mitochondrial proteins, COX5a, complex III core protein 2 and SDHb were down regulated. A reduction in CS in the present study suggests that there are fewer actively respiring mitochondria, however no change in mitochodnrial respiration was noted. A reduction in LEAK respiration as an indicator of reduced mitochondrial uncoupling may be associated with increased ROS production. A significant positive correlation between the reduction in maximal ETS and insulin sensitivity suggests a relationship between the two. The mechanisms involved in disuse muscle atrophy require further clarification, as do the mechanisms linking insulin sensitivity, mitochondrial function and muscle atrophy.