Laser capture microdissection (LCM) allows for the isolation of small tissue fractions from heterogeneous tissue sections, for downstream genetic or proteomic analysis without contamination by the surrounding tissue. This technique can also be successfully used for the isolation of small tissue fractions from developing embryos, such as expanding blastocysts. However, the small size of early-stage embryos hampers tissue processing prior to LCM. The present protocol describes the application of LCM to isolate specific cell fractions from blastocysts for downstream gene expression analysis with RT-PCR.