Methylation of CpG dinucleotides (5meC) within the genome is a key epigenetic determinant which has important roles in the regulation of mitotically heritable patterns of gene expression and genome stability. Fertilisation causes the epigenetic settings within the gametes to be reprogrammed in the new embryo to encode totipotency. A long standing paradigm of this reprogramming of CpG methylation has recently come under question and a new synthesis of this process is emerging. Recent evidence points to some loss of methylation from the paternally-derived (sperm) genome so that by the time of syngamy both the maternally- and paternally-derived genomes have similar levels of methylation. The global methylation levels remain relatively stable for the next several cell-cycles, with no evidence for the previously reported passive global loss of 5meC. With compaction of the embryo, the inner cells begin to lose methylation but it is maintained in the outer cells. By the morula stage, cells encased in an inner position show a ~ 50% reduction of immuno-detectable global levels of 5meC and a further loss occurs in the inner cell mass (ICM) of blastocysts. High levels of 5meC persist in the outer cells of the morula and the resulting trophectoderm of the blastocyst stage embryo. The demethylated state of the totipotent ICM persists as it differentiates into the pluripotent epiblast (UTF1-positive) and multipotent hypoblast (GATA6-positive), while the relatively high levels of the 5meC persist with differentiation of the trophectoderm into trophoblast and trophoblast giant cells (CDX2-positive). Experimental analysis shows that global hypermethylation of the trophectoderm genome compared to the ICM is required for the normal differentiation to this lineage. This new understanding of the normal epigenetics of embryo development provides a firm basis for assessing the requirements for growing healthy embryos.