Our organism and the expression of our genetic inheritance are conditioned by the environment. This is demonstrated by experimental models on animals, but more and more evidence shows similarities also in humans. Evidence now supports that neonatal and maternal health also depends on the interactions between the environment and the DNA itself. Even though the DNA sequence remains the same over the years, some genetic traits of human beings can be affected by the silencing or activation of some nucleotide sequences, for example by DNA methylation. Today, epigenetics is much more important than we used to think in 1942 when Waddington used the word “epigenetics” for the first time. The environment can modify DNA sequence methylation, affecting protein production and the phenotype. Examples of how epigenetics affects childbirth phenomenon are given and mechanisms are discussed. Four biological mechanisms of epigenetics are presented: genomic imprinting and silencing of the paternal set of chromosomes, the unpredictable “on/off” expression patterns of wild type genes, paramutations, and alternative states of protein folding. Some genes are triggered by stress, maternal nutrition, drugs (namely oxytocin, fentanyl), childbirth modalities, labor, environmental behavior, microorganism colonization. Imprinting theory is a good scientific basis, to explain the permanence of some biological effects at a considerable time after birth. Imprinting is an important mechanism of DNA expression, and different types of imprinting are described. The consequences of antibiotic use in the childbirth period are discussed, along with the importance of awareness in the use of antibiotics for maternal prophylaxis. Prenatal antibiotics and cesarean sections do affect neonatal microbiome considerably and, therefore, may be the causes of inflammatory intestinal disorders, asthma, obesity, diabetes. Mode of delivery, labor, breastfeeding, and skin-to-skin practice are strictly related to future neonatal health, and the effects are shown here. One of the most important factors to explain the diseases mentioned above is probably the lack of “bacterial contamination” through the birth canal. However, this mechanism cannot be the only one to act, and, in fact, here we also discuss other mechanisms that contribute to the development of future pathologies. Last but not least, the culture and education of the operators, as well as maternal and providers’ attendance behavior during childbirth, can change the relative outcomes of children’s long-term health.