Physical exercise produces several adaptive changes in skeletal muscle. However, the molecular mechanisms of these effects are poorly understood. We performed serial analysis of gene expression (SAGE) to quantify the global gene expression profile in sedentary and endurance-trained muscle. A total of 10869 SAGE tags was sequenced and represented 4727 genes. The genes most expressed in muscle are mainly involved in contraction and energy metabolism. Thirty-three genes were differentially expressed between endurance athletes and sedentary individuals. Four genes such as myosin binding protein C fast-type, glycogen phosphorylase, and pyruvate kinase were expressed less in endurance athletes, whereas eight genes coding for expressed sequence tag similar to (EST) crystallin alpha B, EST myosin light chain 2, EST surfactant pulmonary-associated protein A1, EST thrombospondin, EST fructose-bisphosphate aldolase A, EST cytochrome oxidase 1, NADH dehydrogenase 3, and G8 protein were up-regulated. Most of the up-regulated tags corresponded to novel genes. On the other hand, different isoforms of fructose-bisphosphate aldolase A were also differentially expressed. The current study underlying the most highly expressed genes allows a better understanding of global muscle characteristics in normal and endurance-trained individuals. Moreover, the current data suggest novel candidate genes that may be responsible for enhanced endurance performance.