This research aimed to retrospectively investigate the possible association between poor ovarian stimulation and selected thrombophilia markers in Iranian women with infertility. For this study 100 Iranian infertile women, with a history of at least three Assisted Reproduction Technology (ART) failures (50 with a poor ovarian response and 50 with a normal response), referred to Royan Institute were selected. Targeted genetic variation evaluation for Factor V G1691A, F II Prothrombin G20210A, MTHFR C677T, MTHFR A1298C was performed by PCR-RFLP followed by Sanger Sequencing. The association between these variants and the ovarian response was examined. The results showed an association between Factor V G1691A mutation and poor ovarian response. The heterozygosity rate of the FVL was significantly different between poor responders compared with the normal response group (p-value ≤ 0.05). In conclusion screening of this polymorphism can be used as a genetic determinant of ovarian response functioning through a vascular mechanism. A larger study with bigger sample size is recommended. Impact statement What is already known on this subject? Thrombophilia is a multi-genetic disease that is associated with changes in homeostatic mechanisms. Some studies have suggested that thrombophilia has no relationship with poor ovarian response and reduced ovarian reserve in general infertile population undergoing ART. What do the results of this study add? Our results showed a significant association between the FVL heterozygote mutation and poor ovarian response. What are the implications of these findings for clinical practice and/or further research? Screening of FVL polymorphism may be suggested as a predictive test for ovarian stimulation response in infertile women undergoing ART. Further prospective studies with bigger sample size evaluating other thrombophilia markers and ovarian response, as well as further in-vitro studies may help clarify the biological mechanisms behind the effect of the FVL polymorphism on ovarian response, oocyte quality and embryo quality.