Cloning efficiency following somatic cell nuclear transfer is very low. In order to obtain insights into this problem, mRNA expression patterns of early development-related genes in nuclear transferred embryos were compared with those obtained from in vivo and in vitro fertilization. Semiquantitative reverse-transcription polymerase chain reaction assay was used to compare the gene expression of, the cell adhesion protein E-cadherin, interleukin -6, heat-shock protein 70.1 and bos taurus apoptosis regulator box-a (Bax). The relative abundances of glucose transporter-1, E-cadherin and interleukin-6 were significantly (P<0.05) higher in in vitro fertilized morulae than in vivo derived morulae. Transcription of the gene encoding octamer-binding transcription factor 4 was higher in blastocysts obtained from in vivo fertilization than in those from in vivo blastocysts. The transcript for Bax was markedly upregulated in blastocysts derived from in vitro production and nuclear transfer procedures compared with in vivo fertilization. These results suggest that alterations in mRNA expression of early development genes are more associated with in vitro culture condition than the nuclear transfer procedure itself.