Problem Aberrant DNA methylation has been suggested as a potential cause of recurrent spontaneous abortion (RSA). Considering the growing evidence on the important roles of DNA methylation in gametogenesis and early pregnancy, we investigated the potential association of DNA methyltransferase gene polymorphisms (DNMT1 rs2228611, DNMT3A rs1550117, DNMT3B rs1569686) with RSA in Slovenian reproductive couples. Method of study A total of 146 couples with ≥3 consecutive spontaneous abortions and 149 control women and men with ≥2 normal pregnancies were included. Genotyping was performed using PCR‐RFLP methods. Results We found a statistically significant higher frequency of the DNMT3B rs1569686 GG genotype (X2=7.37;P = .025) and G allele (X2 = 6.33;P = .012) in RSA women compared with controls. Moreover, the odds for RSA in women were increased under the recessive genetic model (GGvsTG+TT: OR=1.92; 95% CI=1.18‐3.09; P = .008). Conclusion DNMT3B rs1569686 gene polymorphism in women might be a genetic marker for the susceptibility to RSA.