Background: Preeclampsia (PE) is a serious pregnancy complication that poses significant health risks to both mothers and babies. Genetic factors like thrombophilia mutations and deficiencies in natural anticoagulants might contribute to its development, but their exact roles are not well understood, especially among Sudanese women. Objective: To assess the relationship between the Factor V Leiden (FVL) thrombophilic mutation and reduced levels of natural anticoagulants Protein C (PC) and Protein S (PS) with the occurrence of PE among Sudanese women. Methods and materials: We conducted a case-control study that included a total of 300 women, divided equally into three groups: 100 with PE, 100 healthy pregnant women, and 100 healthy non-pregnant women. To detect FVL mutations, we used PCR-RFLP analysis. Levels of PC and PS were measured using colorimetric assays. We applied logistic regression analyses to assess the relationships between these variables and the risk of developing PE. Results: Our findings showed no significant link between FVL mutations and PE (p=.390). PC levels on their own did not emerge as significant independent predictors of PE (OR 1.01, 95% CI 0.99–1.02, p=.419). However, women with low PC and S levels were strongly associated with PE in both univariate and multivariate analyses (OR 77.67, 95% CI 8.97–672.5, p<.001). This combination was significantly more common in the PE group than in the control group (p<.001). Additionally, reduced PS levels were significantly associated with an increased risk of PE. Conclusion: Combined PC/PS deficiencies are strongly associated with PE among Sudanese women, indicating a significant role of these natural anticoagulants in the disease's pathogenesis. FVL mutation was not significantly linked with PE in this population.