While it is known that sulfur containing amino acids (SCAA) are very important in regulating hepatocyte growth and preventing liver-diseases, the fundamental molecular mechanisms of how they exert their hepatoprotective functions are not well known. Since it is widely understood that the hepatic concentrations of S-adenosylmethionine (SAMe) in chronic liver disease patients are severely decreased, the pathophysiological importance of SAMe and its downstream antioxidant, glutathione should be discussed in order to see a big picture of relationship between SCAA and liver diseases. Chronic SAMe deficient mice have shown spontaneous hepatocellular carcinoma development due to impaired mitochondria functions with low levels of prohibitin1 protein, and through deficiency in many genes which are known to ameliorate genetic instability, such as APEX1 and DUSP1, the functions of which are recovered by SAMe treatment. In this review, current knowledge of the basic concepts of the mechanisms through which SCAAs protect the liver will be discussed in detail. Also, a possible tumor suppressor in livers, prohibitin1, and its functional relationship with SAMe will be discussed.