Although inter-species SCNT may be useful for increasing and preserving populations of endangered species, there are many reports that inter-species nuclear transfer embryos only develop to the blastocyst stage. In this study, yak-bovine SCNT blastocysts were successfully implanted in the surrogate bovine uterus but failed to develop to term or aborted. To clarify the reasons, we examined yak-bovine SCNT blastocyst development, total cell number, inner cell mass (ICM) number, trophoblast (TE) cell number and relative gene expression in yak fibroblast cells and yak-bovine SCNT embryos at various stages. The potential for development of yak-bovine SCNT embryos to blastocysts was 30+/-5.7% (mean+/-S.E.M.); the total cell number was 85.3+/-16.3, fewer than in IVF bovine embryos (106.2+/-18.2) but within the reported range (60-300). The yak-bovine SCNT blastocysts had a lower ratio of TE cells to total cells (43.9+/-8.7%) than bovine IVF embryos (59.4+/-3.4%; P<0.05) or bovine-bovine SCNT (69.5+/-5.4%; P<0.05). Also, several yak-bovine SCNT embryos had abnormal initiation of expression of both Mash2 and IL6. However, expression of vimentin, collagen, Cx43 and PSMC3 were normal in yak fibroblast cells and yak-bovine SCNT embryos. In conclusion, we inferred that the normal allocation of ICM and TE cells in yak-bovine SCNT embryos and embryo-specific gene reprogramming may be important for successful inter-species animal cloning.