Significance Dietary folate deficiency is associated with fetal neural tube defects, psychological disorders, and age-associated dementia. However, it remains unclear how folate deficiency could be a causative factor in such a diverse range of disorders. Through analysis of the FRAXA locus, which contains an extensive CGG repeat sequence, we show that folate deprivation triggers extensive mitotic missegregation of the locus. Moreover, the entire chromosome X becomes unstable during a period of long-term folate deprivation. Considering that the human genome contains several loci associated with extensive CGG repeat regions, these findings suggest a mechanism by which folate deficiency contributes to the onset of a wide range of human diseases.