To assess methyl-group metabolism in the central nervous system in infection with human immunodeficiency virus (HIV), levels of 5-methyltetrahydrofolate, methionine, and S-adenosylmethionine were measured by high-performance liquid chromatography in cerebrospinal fluid (CSF) from six children with congenital HIV infection and neurological complications. Total neopterins were also measured, as a marker of macrophage activation. In all six children concentrations of one or more methyl-group carriers were lower than those in a reference population of children, and all of the five in whom CSF neopterins were measured had higher than normal levels. Defective methylation may play a part in the neurological damage caused by HIV infection.