Human embryo development occurs through a process that encompasses reprogramming, sequential cleavage divisions and mitotic chromosome segregation and embryonic genome activation. Chromosomal abnormalities may arise during germ cell and/or pre-implantation embryo development, and are a major cause of spontaneous miscarriage or birth defects. Nonetheless, model systems suitable for the study of human germ cell and embryo development have been limited until recently. We suggest that human embryonic stem cells may provide a valuable human cell-based model for genetic studies of human pre-implantation pluripotent cells. Here, we review the current literature on diagnosing chromosomal abnormalities in the pre-implantation embryo, and the importance of provisions from the human oocyte in establishing and maintaining the human embryonic genome during the first 3 days post-conception. We focus on transcriptional analysis of human oocytes and embryos and the unique cell cycle and checkpoint requirements in the early embryo. Taken together, data suggest that the unique programs of the early human embryo, including management of aneuploid cells, may paradoxically promote embryo development but contribute to the high rate of spontaneous miscarriages in human pregnancies.