Abnormalities of development potential arising from pre-implantation environment are not limited to in vitro culture (IVC) (for, i.e. in ruminants the large offspring syndrome produced by IVC), they may also be consequence of specific stress conditions experienced in vivo, like maternal diet, toxins, etc. A complex group of mechanisms (gene expression, epigenetic, metabolic, etc.) may operate to link early embryo environment with future health. Furthermore, during the pre-implantation period, in vitro produced male embryos have a higher metabolic rate, they grow faster than females, and they also have differential gene transcription of genes located in the Y-, X-, or in autosomal-chromosomes. As a consequence of these differences embryos may be affected differentially by natural or artificial environmental conditions, depending on their gender. It has been suggested that under some stress conditions male embryos are more vulnerable than females; however the biological fragility of male embryos is poorly understood. Evidences suggest that epigenetic differences produced by the presence of one or two X-chromosomes are the principal cause of the male and female pre-implantation differences, and we put forward the possible role of these early sex differences to control sex ratio of the offspring under different environmental conditions in Nature. By following the differences between male and female early embryos not only may be possible to manipulate sex ratio in farm animals, we can also gain further insight into aspects of early embryo development, X inactivation, and epigenetic and genetic processes related with early development that may have a long-term effect on the offspring.