The reported correlation of defects in 5,10-methylenetetrahydrofolate reductase (MTHFR), the key enzyme of folate metabolism, with modulated risk for acute lymphoblastic leukemia (ALL) is ambiguous. We have elucidated the influence of MTHFR genotype on ALL development and relapse in 140 Slovenian pediatric ALL patients and 183 healthy controls. A decreased proportion of low activity MTHFR genotypes was found in a group of ALL patients with relapses compared to healthy controls (p = 0.022) and ALL cases without relapse (p = 0.027). Mutations in the MTHFR gene decrease the onset risk of ALL with relapse in the setting of no folate supplementation in pregnancy, but not of relapse-free ALL.