Developmental abnormalities associated with the cloning process suggest that reprogramming of donor nuclei into an embryonic state may not be fully completed in most of the cloned animals. One of the areas of interest in this regard, is the analysis of gene expression patterns in nuclear transfer (NT) embryos to dissect the processes that failed and develop means to overcome the limitations imposed by these factors. In this study, we investigated expression patterns of histone deacetylase‐1, ‐2, ‐3 (HDAC‐1, ‐2, ‐3), DNA methyltransferase‐3a (DNMT3A), and octamer binding protein‐4 gene (OCT4) in donor cells with different cloning efficiencies and NT embryos derived from these cells employing a real‐time RT‐PCR assay. All genes investigated followed altered expression patterns in NT embryos when compared to IVF‐derived embryos. In general, expression of HDAC genes was elevated especially at the compact morula stage and comparable to in vitro fertilized (IVF) embryos at the hatched blastocyst stage. DNMT3A expression in NT embryos was lower than IVF embryos at all stages. Oct‐4 transcript levels were also reduced in cloned compared to IVF embryos at the compact morula and blastocyst stages. This difference disappeared at the hatched blastocyst stage. There was a donor cell effect on the expression patterns of all genes investigated. These results demonstrate altered gene expression patterns for certain genes, in cloned cattle embryos from our donor cells of different efficiency in producing live offspring. Therefore we suggest that differences in expression of developmentally important genes during early embryo development may characterize the efficiency of donor cells in producing live offspring. Mol. Reprod. Dev. 74: 18–27, 2007. © 2006 Wiley‐Liss, Inc.