A classical model of epigenetic reprogramming of methyl-cytosine-phosphate-guanine (CpG) dinucleotides within the genome of the early embryo involves a process of active demethylation of the paternally derived genome immediately following fertilisation, creating marked asymmetry in global cytosine methylation levels in male and female pronuclei, followed by passive demethylation of the maternally derived genome over subsequent cell cycles. This model has dominated thinking in developmental epigenetics over recent decades. Recent re-analyses of the model show that demethylation of the paternally derived genome is more modest than formerly thought and results in overall similar levels of methylation of the paternal and maternal pronuclei in presyngamal zygotes, although there is little evidence for a pervasive process of passive demethylation during the cleavage stage of development. In contrast, the inner cell mass of the blastocyst shows some loss of methylation within specific classes of loci. Improved methods of chemical analysis now allow global base-level analysis of modifications to CpG dinucleotides within the cells of the early embryo, yet the low cost and convenience of the immunolocalisation techniques mean that they still have a valuable place in the analysis of the epigenetics of embryo development. In this review we consider the key strengths and weaknesses of this methodology and some factors required for its valid use and interpretation.