The neurologic complications of cystathionine beta-synthase deficiency are thought to be secondary to accumulation of homocyst(e)ine in the CNS. Treatment of this disorder with betaine has been shown to improve the behavior of individuals, to reduce plasma total homocysteine, and to correct secondary abnormalities of serine. To test the hypothesis that homocyst(e)ine accumulates within the CNS and that this can be reduced by treatment with betaine, we measured total homocysteine and related metabolites in the plasma of 10 children with cystathionine beta-synthase deficiency and cerebrospinal fluid of five children before and during betaine therapy. In plasma, betaine significantly lowered total homocysteine (but not to the normal range) and had a variable effect on methionine. In the cerebrospinal fluid, total homocysteine was raised before treatment (mean 1.2 microM) and was significantly reduced by betaine (mean 0.32 microM) but not to the normal range (<0.10 microM). Cerebrospinal fluid methionine was raised before and during treatment, but betaine did not cause a significant further increase. Cerebrospinal fluid serine was significantly reduced before treatment and rose to the normal range with betaine. Cerebrospinal fluid S-adenosylmethionine was normal before treatment and rose significantly with treatment; there were no significant changes in cerebrospinal fluid 5-methyltetrahydrofolate. The demonstration of accumulation of homocysteine within the CNS lends support to the hypothesis that this may be one cause of the neurologic complications of cystathionine beta-synthase deficiency. Betaine is effective in reducing cerebrospinal fluid homocysteine, but concentrations are still significantly raised during treatment.