In multivariable analysis of patients aged < 35 years, MTHFR 677CT (adjusted OR, 1.227; 95% CI, 1.064–1.414) and TT (adjusted OR, 1.421; 95% CI, 1.121–1.802) were positively associated with the risk of vitamin D deficiency compared with CC. Here, MTHFR is linked to vitamin D deficiency.