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Infertility is a major issue at present and is a common disease that exists in both male and female reproductive systems, described as failure to attain pregnancy. The most important physiological phenomenon for establishing clinical pharmacy is defined as female infertility (FI). Obesity enhances the risks for many chronic disorders, especially causing a high risk for women's reproductive health. The relationship between infertile women and thrombophilia is characterized by abnormal blood coagulation. Among the thrombophilic variants, Factor V Leiden (FVL), prothrombin (PT) and methyl tetrahydrofolate reductase (MTHFR) in genes such as G1691A (rs6020), G20210A (rs1799963) and C677T (rs1801133) are commonly studied in the majority of human diseases. In this case–control study, we investigated the role of thrombophilic variants such as G1691A, G20210A and C677T in the FVL, PII and MTHFR genes in Saudi infertile women. Based on sample size calculation, 100 female infertile and 100 control (fertile) women were selected based on inclusion and exclusion criteria. Genotyping was performed with polymerase chain reaction and followed with precise restriction enzymes, which can accurately detect the nucleotide amendment variants in G1691A, G20210A and C677T. The required statistics were applied between the case (infertile) and control (fertile) women to document the role of the G1691A, G20210A and C677T variants in Saudi infertile women. In this study, age, weight and BMI were found to be high in the control women in comparison to the infertile women. None of the genotypes, genetic models or allele frequencies were associated with G1691A, G20210A or C677T SNPs (p > 0.05). Furthermore, the regression model and ANOVA analysis also showed negative statistical associations. The combination of genotypes and allele frequencies among G1691A, G20210A and C677T SNPs showed positive associations in the recessive model (p = 0.0006). Finally, the GMDR model showed moderate associations with the gene–gene interaction, dendrogram and depletion models. Finally, this study confirmed that thrombophilic SNPs have no role and may not be involved in Saudi infertile women. [ABSTRACT FROM AUTHOR]