Despite its wide-spread use, the success rate of assisted reproductive technologies including in vitro fertilization is less than 20%. Most human embryos are mosaic for chromosome abnormalities: containing cells that are euploid (normal) and aneuploid (incorrect number of chromosomes). Mosaicism is thought to account for the high rates of early pregnancy loss in IVF and natural conceptions. Currently, a cell biopsy is used in the IVF clinic to diagnose aneuploidy in the embryo. However, this does not provide an accurate diagnosis of how many cells are aneuploid. Hence, the development of a non-invasive tool to determine the proportion of aneuploid cells would likely improve IVF success. Aneuploidy in human embryos leads to altered metabolism. Co-factors utilised in cellular metabolism are autofluorescent and can be used to predict the metabolic state of cells. In this study, we utilised a powerful model of embryo mosaicism where mouse embryos were treated with reversine, a reversible spindle assembly checkpoint inhibitor, from the 4- to 8-cell stage. Eight-cell embryos were then dissociated and euploid and aneuploid blastomeres joined to generate euploid, aneuploid and chimeric blastocysts at different ratios. Blastocysts were fixed and assessed by 65-channel hyperspectral microscopy (broad spectral profile) providing an alternative to metabolomics through non-invasively assessing intracellular fluorophores. Using hyperspectral imaging, we were able to identify type I and type II collagen and the co-enzymes NAD(P)H and FAD which together give us the redox ratio (an important measurement of metabolic activity). In euploid embryos, the abundance of NAD(P)H and the redox ratio were significantly higher compared to 1:1 and 1:3 (euploid:aneuploid) chimeric embryos. Using textural-based analysis, euploid, aneuploid and chimeric embryos showed discrete separation by principle component analysis. These data show hyperspectral imaging is able to distinguish cells based on their ploidy status making it a promising tool in assessing embryo mosaicism.