Fatty acid oxidation in mitochondrial matrix is a major source of energy in muscle, especially when physiological energy demand is increased and exceeds what can be provided through glycolysis. Not surprisingly, a group of muscle disorders due to defects in this system usually leads to the development of acute rhabdomyolysis in conditions such as infection, fasting and prolonged exercise. This group includes beta-oxidation cycle defects and deficiencies of carnitine palmitoyltransferase II (CPTH) and very-long-chain acyl-CoA dehydrogenase (VLCAD). Muscle pathology is usually not very helpful for the diagnosis but immunohistochemistry may be useful for screening VLCAD deficiency. Another group of lipid dysmetablolism is lipid storage myopathy (LSM) that is pathologically characterized by increased lipid droplets both in number and size in muscle fibers. So far, causative genes have been identified in four different LSMs, comprising primary carnitine deficiency, multiple acyl-CoA dehydrogenase deficiency or glutaric aciduria type II, neutral lipid storage disease with ichthyosis, and neutral lipid storage disease with myopathy. Clinically, the LSM patients show slowly progressive muscle weakness unlike the former group. Final diagnosis is usually made by specific biochemical assays with mutation analyses. As some effective drugs have been widely used and some promising therapies are under certified, comprehensive understanding of these diseases from clinical, pathological and molecular aspects would be of much help for the patients.