Preimplantation development is critical for successful implantation and pregnancy. In the mouse preimplantation embryo, the first event of morphological and cellular differentiation is established during polarization and compaction at the 8-cell stage. The considerable cell surface and cytoplasmic changes and formation of different populations of cells at the 8-cell stage are fundamentally important for the development of all organisms. To determine genes that are specifically expressed at this crucial stage of embryo development and also to shed light on the different mechanisms that could be of importance during embryo development, we investigated mouse 8-cell and 4-cell embryo stage-specific genes using Digital Differential Display (DDD). The 8-cell stage-specific genes were sorted according to their ontology data from the Database for Annotation, Visualization and Integrated Discovery (DAVID), which outlines possible roles for the genes expressed at the 8-cell stage. This study highlights how online tools can be used to identify genes involved in embryo development. Identification of the 8-cell embryo stage-specific genes would open new opportunities for understanding molecular networks during the mid-preimplantation gene activation. Using bioinformatic tools, such as Digital Differential Display and DAVID, it will be possible to identify genes expressed at the 8-cell stage that are likely to be involved in mammalian preimplantation embryo development. Our results may provide a new foundation for molecular control at the onset of embryonic development in mammals, and should be of interest to the scientific community.