DNA methylation involves biochemical modification of DNA by addition of methyl groups onto CpG dinucleotides, and this epigenetic mechanism regulates gene expression in disease and development. Mammalian DNA methyltransferases, DNMT (DNMT1, DNMT3A and DNMT3B), together with the accessory protein DNMT3L establish specific DNA methylation patterns in the genome during gametogenesis, embryogenesis and somatic tissue development. The present study addresses the structural and functional conservation of the DNMT in humans, mice and cattle and the patterns of mRNA abundance of the different enzymes during embryogenesis to improve understanding of epigenetic regulation in early development. The findings showed a high degree of structural and functional conservation among the human, mouse, and bovine DNMT. The results also showed similar patterns of transcript abundance for all of the proteins at different stages of early embryo development. Remarkably, all of the DNMT with an important role in DNA methylation (DNMT1, DNMT3A, DNMT3B, and DNMT3L) show a greater degree of structural similarity between human and bovine than that between human and mouse. These results have important implications for the selection of an appropriate model for study of DNA methylation during early development in humans. © 2010, Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.