Biopsy is used for the diagnosis when treating miscarriage. However, it does not guarantee that a healthy oocyte will be acquired. The study aimed to identify proteins that are specific for pregnancy development and determine rDNA in the maternal and fetal genomes during embryogenesis. A total of 45 patients took part in the continuous prospective survey. Non-viable pregnancy was terminated in 25 patients. Another five underwent abortion due to teratogenic effects. Artificial abortion was performed in 15 cases (controls). To quantify proteins, tissues of the chorion and/or embryo and the decidua were collected from all the assessed individuals during surgery, along with blood from the cubital vein. DNA was isolated from all samples by the extraction method involving the use of organic solvents. The rDNA copy number in the DNA was determined by non-radioactive quantitative hybridization (NQH), and the chorion proteins were determined by panoramic mass spectrometry. In individuals with frozen pregnancy, decreased levels of some proteins specific for pregnancy, beta-1-glycoproteins (PSG), were revealed. The rDNA content was the same in blood cells and decidual cells of the same woman. Frozen pregnancy is associated with severe imbalance of the rDNA content in the embryonic and maternal genomes. In most cases, there are significantly less rDNA copies in the embryonic genome, than in the maternal genome and genomes of other embryos, the development of which has not been spontaneously interrupted. Thus, determination of specific proteins in chorionic villi and the rDNA copy number in the potential parents’ genomes with subsequent rDNA copy number modeling in the embryo can help determine possible causes of infertility in married couples and improve the prenatal diagnosis quality.