mtDNA variation in embryos and their effect on early embryo development remains poorly understood. Whole genome amplification (WGA) of trophectoderm (TE) biopsy(4-6-cells) is used in preimplantation embryo testing, allowing for downstream analysis. I optimized mtDNA heteroplasmy detection in WGA TE biopsies and applied this pipeline to a cohort of six motherembryo-product-of-conception cases. Inherent technical bias in coverage and base amplification accuracy of two WGA-systems was evaluated in a set of controlled experiments. RepliG-WGA resulted in uniform amplification of mt-genome, in contrast to uneven amplification by SurePlex. A heteroplasmy detection threshold of >5% was established to minimize false positive SNVs. Using this pipeline for mt-DNA analysis of clinical samples, I identified a high frequency of heteroplasmic variants (2.65±2.7) segregating from mother to embryos and corresponding miscarried fetal samples. Findings highlight the need for optimized heteroplasmy detection in WGA embryonic samples and provide a preliminary insight into mtDNA variation related to IVF outcomes.