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Relevance. A key factor influencing the effectiveness of assisted reproductive technology programmes is the quality of the embryo transferred into the uterine cavity. The aim is to investigate the possibility of using quantitative assessment of genomic (gDNA), mitochondrial DNA (mtDNA) levels in spent culture medium (SCM) and mtDNA in the trophectoderm (TE) as a marker of successful implantation and pregnancy lasting more than 12 weeks. Materials and Methods. The study included 195 SCM samples from 93 couples with infertility. Frozen embryo transfer (FET) was performed in 43 patients. The level of gDNA, mtDNA in SCM by real-time PCR and mtDNA in TE by NGS was analysed depending on the chromosomal status of embryos and the outcome of FET. Statistical analyses were performed in Jamovi software. Results and Discussion. Depending on the outcome of transfer, the patients were divided into groups: Group 1—negative result, n=18; Group 2—pregnancy continuing for more than 12 weeks, n=25. mtDNA and gDNA in SCM were statistically significantly lower in group 2 compared to group 1 (p=0.007 and p=0.01, respectively). When mtDNA levels in SCM were 95 copies, the odds of pregnancy rate and ongoing pregnancy were increased 3.2-fold (95 % CI=1.1–31.6). Prediction formulas for the probability of ongoing pregnancy after FET were proposed for continuous (sensitivity was 67.0 %, specificity was 91 %, area under the curve (AUC) was 90.0 %) and binary (sensitivity was 75.0 %, specificity was 70 %, AUC was 83.8 %). Thus, the level of gDNA and mtDNA copy number in the embryo culture medium is a significant prognostic factor for the onset and prolongation of pregnancy in ART programmes. Depending on the ploidy of the blastocysts, we analysed the level of mtDNA in TE, gDNA and mtDNA in the SCM of embryos in groups 1.1. (euploid, n=98) and 2.1. (aneuploid, n=97). No differences were detected in the compared groups. Conclusion. Assessment of gDNA and mtDNA levels in SCM may be an additional non-invasive marker for selection of the most promising euploid embryo for transfer into the uterine cavity.