Epigenetic modifications of the genome play a significant role in the elaboration of the genetic code as established at fertilisation. These modifications affect early growth and development through their influence on gene expression especially on imprinted genes. Genome-wide epigenetic reprogramming in germ cells is essential in order to reset the parent-of-origin specific marking of imprinted genes, but may have a more general role in the restoration of totipotency in the early embryo. In a similar way, on somatic nuclear cloning, a differentiated cell must become 'reprogrammed' restoring totipotency in order to undergo development. Here we discuss the dynamic epigenetic reprogramming that takes place during normal development and highlight those areas with relevance to somatic nuclear cloning and the possibility of improving the efficiency of this process. We propose the concept of 'epigenetic checkpoints' for normal progression of development and the loss of totipotency.