Objective: We aimed to identify factors that significantly influence the development of thromboembolism during pregnancy and in the postpartum period among factor V Leiden carriers. Methods: A controlled retrospective study was performed on 301 pregnancies of a cohort of 145 FVL-carrier women. Data of individual pregnancies, deliveries, complications including thromboembolism in the index pregnancy and prophylaxis were obtained by structured interview and by review of case-notes. Full-length thrombosis prophylaxis was employed in forty-eight pregnancies. Logistic regression analysis was performed to identify factors that significantly influence the occurrence of deep vein thrombosis or thromboembolism during pregnancy and in the postpartum period. Results: Two-hundred out of the 301 pregnancies ended with childbirth and there were 40 spontaneous abortions. Preterm birth, preeclampsia, placental insufficiency, intrauterine growth retardation, placental abruption, premature rupture of the membranes, uterine inertia, Caesarean section, febrile complication and major haemorrhage occurred in 29, 13, 27, 9, 4, 14, 12, 33, 10 and 7 cases, respectively. Twenty-five pregnancies were complicated by deep vein thrombosis (DVT) or thromboembolism. Thirty-six pregnancies were conceived with past history of deep vein thrombosis and 43 pregnancies were carried in the presence of combined thrombophilia. Prophylaxis alone did not affect the occurrence of pregnancy associated DVT among factor V Leiden carriers (p = 0.2571). Prophylaxis did not affect the occurrence of DVT among women with a history of DVT (p = 0.7199) or among those without a history of DVT (p = 0.1077), however, in the latter group, DVT occurred only when no prophylaxis was given. Pregnancy associated DVT was strongly associated with combined thrombophilia among factor V Leiden carriers (p = 0.0001). Among pregnancies that ended with a Caesarean section (18 without prophylaxis, 15 with prophylaxis) DVT occurred only when no prophylaxis was given (5 cases, p = 0.0267). In a logistic regression model, factors that significantly influenced the development of deep vein thrombosis included gestational age (OR = 1.058, p = 0.0089), the use of thrombosis prophylaxis (OR = 0.118, p = 0.0227) and the presence of combined thrombophilia (OR = 5.835, p = 0.0005). The frequency of premature rupture of the membranes and Caesarean section was significantly higher in those pregnancies in which thrombosis prophylaxis was employed (OR = 7.102, 0.027; OR = 4.129, p = 0.0378, respectively). Conclusion: Thrombosis prophylaxis decreases the risk of pregnancy associated DVT among factor V Leiden carriers. The effect increases with the length of gestation and is significant when combined thrombophilia is present or delivery is affected by Caesarean section. Selective thrombosis prophylaxis among pregnant factor V Leiden carriers might be the presence of combined thrombophilia and Caesarean section.