Background: Thrombosis is one of the most common complications in cancer patients, however the effect of thrombophilic polymorphisms on cancer specific survival is still unclear. Objectives: The aims of the study were to analyze the effect of factor V Leiden (FVL), prothrombin (PT) G20210A, and methylenetetrahydrofolate reductase (MTHFR) C677T polymorphisms on disease-free survival (DFS) in breast cancer and to evaluate the proportional odds model. Methods: Relationship between thrombophilic polymorphisms and DFS was evaluated in 197 breast cancer patients. Data regarding patient's age, menopausal status, tumor size (T), lymph node status (N), cancer stage, tumor grade (G), estrogen and progesterone receptors, c-erbB2 expression, MTHFRC677T, FVL, and PTG20210A polymorphisms in DFS were examined by log-rank test and multivariate analyses. The proportional odds model was tested as an alternative to Cox model because of its insufficient proportional hazards assumption. Results: According to log-rank test, T, N, G, tumor stage, and c-erbB2 were associated with DFS. T, N, G, and c-erbB2 were significantly related to DFS by log-normal regression model. PTG20210A, MTHFRC677T and FVL polymorphisms were not related to DFS in breast cancer (P>0.05). Conclusion: Our study suggests that thrombophilic polymorphisms are not associated with DFS when the proportional odds model is applied.