Background. The role of viruses in spontaneous abortion (SA) in not completely known. Methods. Merkel cell polyomavirus (MCPyV) and Human papillomavirus (HPV), two small DNA tumor viruses, were investigated in SA. MCPyV/HPV DNAs were investigated by PCR and droplet-digital/quantitative PCRs (ddPCR/qPCR) in chorionic villi and peripheral blood mononuclear cells (PBMCs) from SA females (n=100), the cases, and voluntary interruption (VI, n=100) of pregnancy females, the controls. Results. MCPyV DNAs were detected in 4% and 5% of SA and VI chorionic villi, respectively, with a mean DNA load of 1.99 copy/104 cells in SA and 3.02 copy/10,000 cells in VI (p>0.05). HPV DNAs were detected in 2% of VI chorionic villi, with a mean DNA load of 7.12 copy/cell. Two cases in the VI samples were HPV-45 positive. In PBMCs, MCPyV DNA was detected in 9% and 14% of SA and VI samples, with a mean viral DNA load of 2.09 and 4.70 copy/10,000 cells in SA and VI samples, respectively (p>0.05). None of PBMCs samples tested HPV-positive. Conclusions. MCPyV and HPV DNAs were quantified, for the first time, by ddPCR/qPCR in SA and VI chorionic villi and PBMCs. Data of the present study may help to better understand the role of MCPyV/HPV in SA.