This chapter focuses on the application and methods used to analyze the embryo's transcriptome. The basic genetic program controlling preimplantation development includes activation of the embryonic genome, compaction, and cell lineage specification, and cavitation or blastocyst formation. Embryonic genome activation encompasses a shift from a repressed state characteristic of oocyte chromatin to a permissive state required for transcriptional activation and embryonic gene expression. Preimplantation embryos from all mammalian species do not represent abundant sources of mRNA. Since the protocols for transcriptome analysis using most omics platforms requires μg quantities of mRNA the application of these methods to defining the preimplantation embryo transcriptome requires the inclusion of a global mRNA amplification step that increases the template sufficiently to enable array hybridization. Due to the more direct assessment of RNA level, qRT-PCR is accepted as the gold standard for validating a microarray dataset.