Aneuploidy is common among preimplantation human embryos used in assisted reproductive technology. Because abnormal chromosome number can negatively affect reproductive outcome, in vitro-fertilized embryos routinely undergo aneuploidy testing before transfer into the uterus. This testing typically involves an invasive trophectoderm biopsy of a blastocyst-stage embryo. However, emerging evidence indicates that, during in vitro development, embryos secrete cell-free DNA into their culture medium; this phenomenon suggests the potential for an alternative, noninvasive assay for aneuploidy. Embryonic cell-free DNA-based assays exhibit high concordance with trophectoderm biopsies, inner cell mass and the whole blastocyst. Yet, informativity and concordance rates may be influenced by several factors: culture day when medium is collected, contamination with external and/or cumulus cell DNA, and previous manipulation of the embryos. In this review, we discuss non-invasive embryonic cell-free DNA analysis as a biomarker to prioritize blastocysts for transfer to help increase implantation rates and reduce miscarriage rates and time to achieve pregnancy. We also discuss ongoing research on the mechanisms underlying embryonic cell-free DNA secretion and how this impacts its role as a biomarker of aneuploidy.