Objectives to evaluate direct oral anticoagulants (DOACs) in patients with hereditary thrombophilia and deep venous thrombosis (DVT). Methods This is a retrospective observational study. Results In total, 45 patients were treated between 01/2012 and 12/2022 (mean follow-up: 1.5 +/− 0.3 years). The most frequent thrombophilias were heterozygous V Leiden (20%), heterozygous MTHFR C677T (37.8%), heterozygous MTHFR A1298C (24.4%), and hyperhomocysteinemia (26.7%). The patients received rivaroxaban ( n = 19), apixaban ( n = 15), and dabigatran ( n = 11). Three cases presented symptoms’ recurrence without evidence of thrombosis’ recurrence (two under rivaroxaban and one under apixaban; p > .05). These patients improved under parenteral anticoagulation and were further treated with dabigatran. No other event or major bleeding occurred during the follow-up. The presence of more than two factors was associated with acute recurrence of symptoms (OR = 25.9; 95% CI [1.454–461.262]; p = .026). Conclusions DOACs seem to be safe and efficient for patients with hereditary thrombophilia and DVT. The presence of more than two thrombophilia factors is associated with a higher risk for symptom recurrence. Although statistically non-significant, symptoms’ recurrence was also observed more frequently among patients under anti-Xa inhibitors than antithrombin inhibitors. This should be verified in larger comparative studies.