The effects of specific components in culture medium on embryo physiology have been extensively investigated to optimize in vitro culture systems; however, little attention has been paid to antibiotics, the reagents used most commonly in culture systems to prevent contamination. To investigate the potential effects of routine use of antibiotics on cultured embryos, mouse zygotes were cultured with or without antibiotics. In both groups, the developmental rate and cell number of blastocysts appear to be normal. The proportion of embryos with blastomere fragmentation increased slightly when embryos were cultured with antibiotics. In contrast, the presence of antibiotics in the embryo culture system significantly disturbs expression of zygotically activated genes, damages chromatin integrity and increases apoptosis of cultured embryos. These results provide evidence that, when cultured with antibiotics, embryos with normal appearance may possess intrinsic physiological and genetic abnormalities. We demonstrate that the adverse effects of antibiotics on mammalian embryos are more severe than we previously presumed and that antibiotics are not essential for sterility of embryo culture system therefore abolishing antibiotic supplementation during embryo culture.