Brain metabolism is in principle similar to the biochemical processes which take place in all cells and organs. However, specialization of the different cell types in the brain, i.e. neurons or glial cells, adds a complexity which differs from other organs. In this chapter, a detailed outline of the metabolic processes providing the basis for brain energy and ammonia metabolism is provided. It also contains information regarding the effects on energy metabolism of a dysfunctional ammonia homeostasis such as that related to hepatic encephalopathy (HE). Moreover, methodological tools by which these metabolic processes may be studied experimentally such as PET as well as tissue and cell preparations are reviewed.