The protocol describes the removal of embryonic cells using a simple manual method that eliminates the need for micromanipulation equipment, followed by sample processing for whole genome amplification, up to the point at which the samples are sent to the genotyping laboratory. Thus, steps required for genomic selection of bovine embryos—from the in vitro fertilization (IVF) laboratory to the genotyping service—are encompassed. Grade I embryos at the blastocyst stage, preferably on day 7 (154–168 h.p.i.), are selected and transferred to biopsy plates containing identified microdroplets, with one embryo per droplet. Using an appropriate microblade, the operator cuts a portion of the trophectoderm from the embryo. The embryo is then cryopreserved, and the excised sample is transferred to a 0.2 mL tube and stored. The second stage of the protocol involves processing the sample by lysing cell membranes to release and denature DNA, followed by amplification of the DNA through an enzymatic reaction. These operations are carried out using a thermal cycler and, by the end of the protocol, yield a sufficient amount of DNA for submission to the genotyping laboratory.