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From Wikipedia
Causes
There are many types of encephalopathy. Some examples include:

Mitochondrial encephalopathy: Metabolic disorder caused by dysfunction of mitochondrial DNA. Can affect many body systems, particularly the brain and nervous system.

Glycine encephalopathy: A genetic metabolic disorder involving excess production of glycine.

Hepatic encephalopathy: Arising from advanced cirrhosis of the liver.

Hypoxic ischemic encephalopathy: Permanent or transitory encephalopathy arising from severely reduced oxygen delivery to the brain.
Static encephalopathy: Unchanging, or permanent, brain damage.

Uremic encephalopathy: Arising from high levels of toxins normally cleared by the kidneys−rare where dialysis is readily available.

Wernicke's encephalopathy: Arising from thiamine (B1) deficiency, usually in the setting of alcoholism.

Hashimoto's encephalopathy: Arising from an auto-immune disorder.

Hyperammonemia: a condition caused by high levels of ammonia, which is due to inborn errors of metabolism (including urea cycle disorder or multiple carboxylase deficiency), a diet with excessive levels of protein, deficiencies of specific nutrients such as arginine or biotin, or organ failure.

Hypertensive encephalopathy: Arising from acutely increased blood pressure.

Chronic traumatic encephalopathy: Progressive degenerative disease associated with multiple concussions and other forms of brain injury.

Lyme encephalopathy: Arising from Lyme disease bacteria, including Borrelia burgdorferi.

Toxic encephalopathy: A form of encephalopathy caused by chemicals, often resulting in permanent brain damage.

Toxic-Metabolic encephalopathy: A catch-all for brain dysfunction caused by infection, organ failure, or intoxication.

Transmissible spongiform encephalopathy: A collection of diseases all caused by prions, and characterized by "spongy" brain tissue (riddled with holes), impaired locomotion or coordination, and a 100% mortality rate. Includes bovine spongiform encephalopathy (mad cow disease), scrapie, and kuru among others.

Neonatal encephalopathy (hypoxic-ischemic encephalopathy): An obstetric form, often occurring due to lack of oxygen in bloodflow to brain-tissue of the fetus during labour or delivery.

Salmonella encephalopathy: A form of encephalopathy caused by food poisoning (especially out of peanuts and rotten meat) often resulting in permanent brain damage and nervous system disorders.

Encephalomyopathy: A combination of encephalopathy and myopathy. Causes may include mitochondrial disease (particularly MELAS) or chronic hypophosphatemia, as may occur in cystinosis.

Creutzfeldt–Jakob disease (CJD; transmissible spongiform encephalopathy).

HIV encephalopathy (encephalopathy associated with HIV infection and AIDS, characterized by atrophy and ill-defined white matter hyperintensity).

Sepsis-associated encephalopathy (this type can occur in the setting of apparent sepsis, trauma, severe burns, or trauma, even without clear identification of an infection).

Epileptic encephalopathies:
Early infantile epileptic encephalopathy (acquired or congenital abnormal cortical development).
Early myoclonic epileptic encephalopathy (possibly due to metabolic disorders).