Background: Recurrent pregnancy loss (RPL) is a common disorder that affects around 3 to 5% of pregnant women. It has different causes, and in about 50%, it is of unknown etiology. Thrombophilia might increase the risk of RPL by adversely affecting the normal placental vascular function. Our study aimed to determine the frequency of factor V Leiden (FVL) and prothrombin G20210A gene mutations in Algerian women with RPL and to correlate their presence with the occurrence of such health's problem. A total of 80 women with previous fetal losses and 100 age-matched women with no history of fetal loss were recorded. Participants were tested for activated protein C resistance (APCR), protein C (PC), protein S (PS), and antithrombin (AT) deficiencies. The screening of FVL and prothrombin G20210A mutations was also done using a duplex polymerase chain reaction. Results: APCR was detected in 6.25% of cases and was absent in controls (p = 0.011). PC and PS deficiencies were documented in 7.5% of patients. FVL was detected in 8.33% of patients and was absent in controls (p = 0.047). Prothrombin G20210A mutation was found in 8.33% of patients compared to 11.11% of controls (p = 0.631). A significant association of FVL mutation with the abortion which occurred in the second trimester was found (p = 0.001). Conclusion: There is a significant association between FVL mutation and RPL especially the loss occurring during the second trimester. No correlation was found regarding prothrombin G20210A mutation.