The present study investigated mRNA expression profiles of bovine oocytes and blastocysts by using a cross-species hybridisation approach employing an array consisting of 15,529 human cDNAs as probe, thus enabling the identification of conserved genes during human and bovine preimplantation development. Our analysis revealed 419 genes that were expressed in both, oocytes and blastocysts. The expression of 1,324 genes was detected exclusively in the blastocyst, in contrast to 164 in the oocyte including a significant number of novel genes. Genes indicative for transcriptional and translational control (ELAVL4, TACC3) were over-expressed in the oocyte, whereas cellular trafficking (SLC2A14, SLC1A3), Proteasome (PSMA1, PSMB3), cell cycle (BUB3, CCNE1, GSPT1) protein modifications and turnover (TNK1, UBE3A) were found to be over-expressed in blastocysts. Transcripts implicated in chromatin remodeling were found in both oocytes (NASP SMARCA2) and blastocysts (H2AFY, HDAC7A). The trophectodermal markers PSG2 and KRT18 were 5- and 50-fold enriched in the blastocyst. Pathway analysis revealed differential expression of genes involved in 107 distinct signalling and metabolic pathways. For example, phosphatidylinositol signalling and gluconeogenesis were prominent pathways identified in the blastocyst. Expression patterns in bovine and human blastocysts were to a large extent identical. This analysis compared the transcriptomes of bovine oocytes and blastocysts and provides a solid foundation for future studies on the first major differentiation events in blastocysts and identification for a set of markers indicative for regular mammalian development.