By the end of the nineteenth century, ammonia had been identified as the main factor responsible for hepatic encephalopathy syndrome. Ammonia is one of the principal products of hepatic metabolism and high concentrations are toxic to the body. Under physiological conditions, the main way by which the body restricts the blood concentration of ammonia to a nontoxic level is by converting it to urea in the liver via the Krebs cycle. The synthesis of glutamine represents an alternative pathway for ammonia detoxification in cirrhotic patients. Although high concentrations of ammonia have been strongly associated with brain edema, estimates of the strength of the correlation between serum ammonia levels and the severity of hepatic encephalopathy vary. The accuracy of ammonia assays depends on the site of specimen collection, treatment of the specimen and the analytical method used. New methods involving measurement of the partial pressure of ammonia and new noninvasive techniques involving quantification of ammonium in the breath have been described. The purpose of this review is to identify factors that affect serum ammonia levels, from its origin and metabolism to its analysis and interpretation of results in the laboratory. In conclusion, variations in estimates of serum ammonia level and the severity of hepatic encephalopathy arise because of individual differences in ammonia metabolism and differences in the accuracy of analytical methods.