Recently reported data clarify our understanding of the molecular aspects of carnitine in medicine. Carnitine is a compound necessary for the transport of acyl-CoA across the inner mitochondrial membrane for their beta-oxidation. Only L-isomer of carnitine is biologically active. The D-isomer may actually compete with L-carnitine for absorption and transport, increasing the risk of carnitine deficiency. By interaction with CoA, carnitine is involved in the intermediary metabolism by modulating free CoA pools in the cell. Detoxification properties and anabolic, antiapoptotic and neuroprotective roles of carnitine is presented. Carnitine deficiency occurs as a primary genetic defect of carnitine transport and secondary to a variety of genetic and acquired disorders. The pathophysiological states associated with carnitine deficiency have been summarized. L-Carnitine is effective for the treatment of primary and secondary carnitine deficiencies. Acetyl-L-carnitine improves cognition in the brain, significantly reversed age-associated decline in mitochondrial membrane potential and improved ambulatory activity. The therapeutic effects of carnitine and acetylcarnitine are discussed.