During mammalian embryonic development, DNA methylation and histone modifications are important in gene expression regulation and epigenetic reprogramming. In cloned embryos, high levels of DNA methylation and abnormal demethylation were widely observed during the preimplantation period. Little is known whether there is a difference in histone modifications between in vitro fertilization (IVF) and cloned embryos during preimplantation development. In the present study, the distributions and intensity patterns of acetylations in H3 lysine 9, 18 and H4 lysine 8, 5 and tri-methyl lysine 4 and dimethyl-lysine 9 in histone H3 were compared in cloned and IVF bovine preimplantation embryos by using indirect immunofluorescence and scanning confocal microscopy. The results showed that the acetylation and methylation levels of H3K9ac, H3K18ac, H4K5ac, H4K8ac, H3K4me3 and H3K9me2 were abnormally high in the cloned embryos from the pronuclear to the 8-cell stage. H4K8ac and H4K5ac in the cloned embryos were particularly abnormal when compared with the IVF controls. At the blastocyst stage differences dissipated between cloned and IVF embryos and the distribution and intensity patterns of all histone modifications showed no obvious difference. These results suggest that somatic cells in recipient oocytes produced aberrant histone modifications at multiple sites before the donor cell genome is activated. After zygotic genome activation, distributions and intensity patterns of histone modifications were comparable with both cloned and IVF embryos.