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Background  Prenatal exposure to essential and non-essential metals impacts birth and child health, including fetal growth and neurodevelopment. DNA methylation (DNAm) may be involved in pathways linking prenatal metal exposure and health. In the Project Viva cohort, we analyzed the extent to which metals (As, Ba, Cd, Cr, Cs, Cu, Hg, Mg, Mn, Pb, Se, and Zn) measured in maternal erythrocytes were associated with differentially methylated positions (DMPs) and regions (DMRs) in cord blood and tested if associations persisted in blood collected in mid-childhood. We measured metal concentrations in first-trimester maternal erythrocytes, and DNAm in cord blood ( N  = 361) and mid-childhood blood ( N  = 333, 6–10 years) with the Illumina HumanMethylation450 BeadChip. For each metal individually, we tested for DMPs using linear models (considered significant at FDR < 0.05), and for DMRs using  comb-p  (Sidak  p  < 0.05). Covariates included biologically relevant variables and estimated cell-type composition. We also performed sex-stratified analyses.    Results  Pb was associated with decreased methylation of cg20608990 ( CASP8 ) (FDR = 0.04), and Mn was associated with increased methylation of cg02042823 ( A2BP1 ) in cord blood (FDR = 9.73 × 10 –6 ). Both associations remained significant but attenuated in blood DNAm collected at mid-childhood ( p  < 0.01). Two and nine Mn-associated DMPs were identified in male and female infants, respectively (FDR < 0.05), with two and six persisting in mid-childhood ( p  < 0.05). All metals except Ba and Pb were associated with ≥ 1 DMR among all infants ( Sidak p  < 0.05). Overlapping DMRs annotated to genes in the human leukocyte antigen (HLA) region were identified for Cr, Cs, Cu, Hg, Mg, and Mn.    Conclusions  Prenatal metal exposure is associated with DNAm, including DMRs annotated to genes involved in neurodevelopment. Future research is needed to determine if DNAm partially explains the relationship between prenatal metal exposures and health outcomes.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13148-021-01198-z.

Prenatal metal exposure, cord blood DNA methylation and persistence in childhood: an epigenome-wide association study of 12 metals