In this prospective cohort study of 1565 community-dwelling Chinese adults, we observed that serum betaine levels were inversely associated with incident of type 2 diabetes after a median follow-up of 8.9 years, while participants who carry heterozygous or homozygous variants of MTHFR G1793A and MTHFR A1298C had a lower risk of incident type 2 diabetes compared with those carried normal type genotypes. This evidence concerns the gene MTHFR and type 2 diabetes mellitus.