After stratification of data, according to gender, a significant association between TLR9 rs5743836 polymorphism and risk of VTE recurrence was found in female patients on univariate Cox regression analysis (HR 3.60 and 95% CI 1.11–11.61, P = 0.033) and on multivariate Cox regression analysis after adjusting for location of DVT, family history of VTE, mild and severe thrombophilia and acquired risk factors for VTE (HR 3.46, CI 1.06–11.33, P = 0.040). Here, TLR9 is linked to Rare hereditary thrombophilia.