Epigenetic marks are established during the embryo development and remain stable in the somatic cells of an adult but are reprogrammed in the germ line to grant pluripotency of future preimplantation embryos. Epigenetic marks that regulate gene expression include DNA methylation, histone variants and histone modifications. Targets of DNA methylation in mammals are almost always CpG dinucleotides. Among CpG islands there is a small number of imprinted germline differentially methylated regions. Genes are imprinted in asymmetrical fashion in male and female embryos. Their marks are maintained after fertilization as a lifelong memory of parental origin of the allele in the new generation. DNA methylation is also used for silencing mobile genetic elements via piRNA pathway proteins and can also be found at other non-imprinted regions. The DNMT3A:DNMT3L complex is the key protein for DNA methylation. Histone modifications which are established by a variety of enzymes and factors determine accessibility of certain regions of the genome to methylation machinery. Together, CFP1 and SETD1 establish the H3K4me3 ''protective'' mark, whereas KDM1B removes it. Transcription helps make certain regions of the genome accessible and helps establish a permissive state of chromatin (H3K36me3) through joining of RNA polymerase with SETD2. ZFP57 is an important factor in both post-fertilization maintenance of methylation and de novo DNA methylation. It is not yet known which factors decide which regions to methylate. Mistakes during methylation and incomplete methylation machinery will most likely lead to non-viable embryos or development of disease in the adult. Inheritance of changed epigenome is possible if germline reprogramming fails. Epigenome can be environmentally altered either by toxicants or by lifestyle.