Isolation of pure inner cell mass (ICM) and trophectoderm (TE) samples from a single blastocyst is necessary to obtain accurate information on the transcriptomes of these cells. Laser capture microdissection (LCM) provides the possibility to isolate small tissue fractions from heterogeneous tissue sections without contamination by the surrounding tissue and without changing the gene expression pattern of the cells. However, the small size of blastocysts hampers tissue processing prior to LCM. This article describes a protocol for the application of LCM to isolate homogeneous ICM and TE cell samples from single bovine blastocysts for downstream gene expression analysis.