It has long been known that, in addition to genetic factors, epigenetic effects fundamentally influence the functioning of the living organism. Although the genome of individual cells of the human body is almost identical, the access, transcription and expression of genetic information are influenced by epigenetic effects. The eukaryotic nuclear DNA is wrapped around histone octamers to form the nucleosome, the basic unit of the chromatin structure. The covalent modifications of the histone proteins cause epigenetic changes. Human conception, followed by the division and implantation of the fertilized egg into the maternal decidua, is a complex process that requires the coordinated functioning of embryological, immunological processes and anatomical structures. The steps of these processes are genetically determined and the coarse- and fine-tuning of these effects occurs at the epigenetic level by external effects such as hormones, toxins, changes in diet, infections, or cell differentiation. The most significant rearrangements occur in the embryonic period after the fertilization of the egg. In our paper, we review the literature to present the effects that influence the fine-tuning of genome function at the epigenetic level. Disturbances of these mechanisms are the basis of several pathologies that threaten conception, implantation and successful pregnancy, such as recurrent miscarriage, preeclampsia, fetal growth restriction or premature birth. In addition, epigenetic alterations acting during the period of plasticity of individual development can cause diseases that appear in the young, adult and even old age of the offspring, which can even be inherited through generations.