Maintaining undifferentiated state and self-renewal ability of embryonic stem cells is a process that many genes and factors participate in. Using bioinformatics analyses and suppression subtractive hybridization we cloned a novel human gene related to the proliferation of human embryonic stem (hES) cells and its mouse homologue and identified them as being borealin. Our data demonstrated that borealin was highly expressed in undifferentiated ES cells, mouse pre-implantation embryos and the brain of 8.5-9.5 day post-coitum mouse embryos. Furthermore, following Borealin depletion by microinjecting anti-Borealin antibody into the zygotes the mouse embryos were arrested at the 2 or 4-cell stage and chromosomes could not correctly localize at the equator plane of the mitotic spindle and most cells had two or more nuclei. Taken together, these results indicate that Borealin plays a crucial role in the early mouse embryonic development.