Real-time, reverse transcription quantitative PCR (RT-qPCR) is a highly sensitive and reproducible technology for the analysis of gene expression patterns. Its ability to detect minute quantities of nucleic acid from multifarious sources makes it an ideal technique for embryonic transcript quantification. However, complex cellular diversity and active transcriptome dynamics in early embryos necessitate particular caution to avoid erroneous results. This chapter is intended to outline basic methodology to design and execute RT-qPCR experiments in pre-implantation embryos.