Abstract Objectives Bechet’s disease (BD) is a multisystem inflammatory disorder with predominant and frequent vascular complications. The pathogenesis of thrombosis in BD is not clearly known, vasculitis and/or multifactorial procoagulant activities are the cornerstone histopathological features of the disease. Patients and methods In this study, we investigated the role of hypercoagulable state and the hemostatic alteration in BD patients and their susceptibility to develop vascular thrombotic complications using ViennaLab CVD StripAssay for molecular detection of thrombophilia gene mutation by PCR and reverse hybridization to allele-specific oligonucleotide probes immobilized on test strip. Natural anticoagulant levels were also assessed to trace the association between activated coagulation system and increased susceptibility of BD patients to develop vascular complication. Results The study revealed a significant association between human platelet antigen-1 polymorphism and the presence of vascular thrombosis, either arterial or venous, in BD patients. Also, there was a significant relationship between mutant MTHFR genotype and venous thrombosis. But, there was an insignificant association between vascular complications in BD patients from one side and the levels of natural anticoagulants (protein C, protein S, and antithrombin III) and mean platelet volume (MPV) level from the other side. Conclusion Despite the association of some thrombophilic factors with the thrombotic tendency seen in BD, the usage of anticoagulants in BD patients with thrombosis may be unnecessary.