Vitrification of embryos is a routine procedure in many IVF laboratories. The effect of vitrification on gene expression and some modifications of H3 histone in H19 and MEST imprinted genes in blastocysts produced in vitro from non-vitrified and vitrified two-cell embryos was investigated. The expression level of the chosen imprinted genes increased significantly (P < 0.05) in experimental groups compared with in-vivo blastocysts (control group). H3K9me2 decreased, whereas H3K9ac increased in the experimental group compared with the control group. The increases in the expression levels of the imprinted genes, and the attendant changes in histone and chromatin status associated with in-vitro culture of embryos from the two-cell stage, are unaffected by prior vitrification and warming. In the present study, it was shown that such changes are solely caused by the effect of in-vitro culture, irrespective of vitrification. Although these genes are sensitive to environmental changes, vitrification seems to have no additional effect on these genes and on the histone marks, and can threfore be considered to be a process with minimum damage for embryo cryopreservation in assisted reproductive technology applications.