Early mammalian embryogenesis is currently the focus of intense interest because of the potential of inner cell mass-derived embryonic stem cell lines in new therapeutic strategies. As such, creating molecular profiles of gene expression during pre-implantation development will provide a framework for understanding the biological properties of these cells and also establish a tool set for subsequent functional studies. However, a major obstacle impeding progress in this area are moral issues regarding their use, the scarcity of these cells and the ability to successfully isolate and amplify enough mRNA from the minute amounts of total RNA present in these cells. The elucidation, unravelling and understanding the molecular basis of transcriptional control during pre-implantation development is of utmost importance if we are to diagnose, intervene, eliminate or reduce abnormalities associated with growth, disease and infertility by applying assisted reproduction. Importantly, these studies should enhance our knowledge of basic reproductive biology and its application to regenerative medicine. This review describes the application of in silico-based approaches, in order to obtain maximal information from published microarray-based gene expression data. For an illustration of this, we used gene expression data related to unfertilized oocytes and blastocysts to gain insights into genes and related signalling pathways (e.g. MAPK, PI3K, WNT, TGF-β) involved in the switch from maternal to embryonic control of gene transcription during human pre-implantation development.