It is widely known that carnitine deficiency can occur due to primary carnitine deficiency (systemic carnitine deficiency) caused by genetic abnormalities of the carnitine transporter, or secondary carnitine deficiency caused by inherited metabolic diseases, including organic acidemias, fatty acid oxidation disorders, and mitochondrial abnormalities, urea cycle disorders and other inherited metabolic diseases such as phenylketonuria and Rett syndrome due to drug administration or restricted protein intake. There are several treatment guidelines and recommendations for these inherited metabolic diseases including Japan, so that the etiology of carnitine deficiency in these diseases and outline of carnitine supplementation therapy are briefly described in this chapter.