Mosaic variegated aneuploidy (MVA) is an autosomal recessive disorder that is characterized by mosaic aneuploidies involving multiple different chromosomes across numerous tissue types. These aneuploidies typically consist of numerous trisomies and monosomies and are caused by mutations in four spindle checkpoint genes: BUB1B, BUB3, CEP57, and MAD2L1. Epigenetic histone modifications are known to influence chromatin structure and are critical in cell cycle progression and cell fate, including the histone-modifying enzyme, MSK2. The objective of this study was to determine if spindle checkpoint gene variants or expression levels of a histone-modifying enzyme are the cause of chromosome chaos (≥3 chromosome errors) in human IVF blastocysts. Research study. DNA extracted from human trophectoderm biopsies was tested for comprehensive chromosome screening including: euploid controls (n=13), trisomy 22 (n=5), trisomy 15 (n=8), young chaotic (maternal age <35 years old; n=13) and old chaotic (advanced maternal age, AMA >40 years old; n=13). Library preparation was performed using the TruSeq® Custom Amplicon Low Input Kit (Illumina) followed by DNA sequencing (Illumina MiSeq®). Reads generated were mapped to the human genome (hg19) and variants were analyzed using Integrative Genomics Viewer software (IGV 2.3, Broad Institute). Gene transcription was assessed using qPCR relative to the house keeping gene, PPIA; and analyzed with REST© statistical software (Qiagen), significance at P<0.05. Targeted sequencing detected variants in all four spindle checkpoint genes: BUB1B, BUB3, CEP57, and MAD2L1. None of the identified sequence variants were considered clinically significant. CEP57 contained the highest number of variants (n=6), while MAD2L1 showed the closest similarities in regards to chromosome complement (n=1 variant). Screening of the four spindle checkpoint genes across the IVF blastocyst groups failed to identify any variant that distinguished chromosome chaos or chromosome constitution. In contrast, MSK2 expression levels were significantly reduced in old chaotic blastocysts compared to euploid controls, trisomy and young chaotic blastocysts (P<0.05), revealing a potential mechanism for chromosome chaos in AMA human blastocysts since reduced MSK2 expression has been shown to prevent the localization and function of cell cycle progression proteins, resulting in aneuploidy generation. Taken together, these data suggest that epigenetic histone modifications which can influence chromatin structure, not spindle checkpoint genes involved in MVA, are associated with the mechanism responsible for chromosome chaos in human blastocysts from AMA infertile patients. Understanding the requirements for normal mitotic chromosome segregation during embryonic development may be applied to clinical improvements in ART.