Paternal overweight/obesity was associated with lower sperm methylation at MEG3, NDN, SNRPN and SGCE/PEG10 and higher methylation at MEG3-IG, H19, IGF2 compared with controls. There was little evidence of association at GRB10, NNAT, PLAGL1, PEG1/MEST, PEG3. Here, MEG3 is linked to obesity due to melanocortin 4 receptor deficiency.