The pathogenesis of the neuropathy associated with vitamin B12 deficiency (subacute combined degeneration (SCD)) is now thought to be related to interference with the methylation reactions in the CNS. The methylation reactions are processed by S-adenosylmethionine (SAM), which is controlled by its product, S-adenosylhomocysteine (SAH). The relationship of these two compounds is termed the methylation ratio. It has been demonstrated that if the ratio falls, the methylation reactions are inhibited leading to a state of CNS hypomethylation. The ratio can fall either due to a rise in SAH or a fall in SAM. It is suggested that for clinical signs to develop in animals who are susceptible to the lesion, both events are usually required. Inhibition of the vitamin B12-dependent enzyme, methionine synthase, leads to a rapid fall in the ratio in the CNS, since unlike other organs such as the liver, it does not have an alternative method of re-methylating homocysteine to maintain the endogenous synthesis of SAM. The supply of methyl groups necessary for the re-methylation reactions is controlled by a series of enzymes, which include methionine synthase. The inborn errors of metabolism that produce deficiency or impairment of these enzymes are described. Neurological syndromes associated with deficiency of these enzymes have close associations with SCD. The other clinical evidence and animal experiments that support this hypothesis are also described.