Abstract Given the difficulties in establishing bona fide porcine embryonic stem cells, we considered it would be interesting to investigate histone modifications, X chromosome inactivation (XCI), deacetylation, DNA methylation, and gene expression around the time of inner cell mass (ICM) and epiblast formation in sexed embryos. We found that the porcine epiblast expressed lower levels of NANOG and C-MYC, of which, we speculate may be one indication for the difficulties in obtaining embryonic stem cells (ESCs) from the porcine embryonic epiblast. Our research revealed distinct expression of lineage-specific-, early gastrulation-, and pluripotency-associated genes between the E10 epiblast and trophectoderm and between sexes. We determined that H3K27me3 was hypermethylated in the E6 embryo and hypomethylated in the E10 epiblast. Interestingly, we also observed exclusive localization of H3K4me3 in the E6 ICM, which may be a key marker for early lineage segregation in the pig. We also observed that the methyltransferases of H3K4me3, H3K27me3 and H3K9me3 and the DNA methyltransferases differed between male and female E10 embryos, and between tissues. We consider that epigenetic mechanisms, which are modified by specific enzymes, may be important for both early lineage segregation events and XCI, and these may further effect the levels of downstream-targeted gene expression in the different sexes.