The neurotoxic effects of therapy for childhood acute lymphoblastic leukemia can result in leukoencephalopathy or measurable deficits in cognitive function. However, there are no validated biomarkers that allow the identification of those patients at greatest risk. With the objective of identifying such predictors, cerebrospinal fluid collected from 53 patients over 2.5 years of therapy for childhood acute lymphoblastic leukemia was retrospectively studied. Cerebrospinal fluid folate, concentrated relative to serum folate prior to therapy, dropped during the first month of therapy and remained below baseline throughout treatment. Cerebrospinal fluid homocysteine was inversely related to cognitive function prior to treatment. Oral methotrexate was associated with decreased cerebrospinal fluid folate and increased cerebrospinal fluid homocysteine, but these changes were not seen with oral aminopterin. Of 36 patients who had imaging after completion of therapy, 9 had periventricular or subcortical white matter abnormalities consistent with leukoencephalopathy. Peak cerebrospinal fluid tau concentrations during therapy were higher among patients who had leukoencephalopathy after completion of therapy than among those with normal imaging studies at the end of therapy. If confirmed prospectively, these markers may allow the identification of those patients at greatest risk of developing treatment-induced neurocognitive dysfunction, thus guiding preventive interventions.