Background: Patients undergoing bariatric surgery are at risk for deep venous thrombosis (DVT) and fatal pulmonary embolus. In the presence of genetic hypercoagulable disorders, accepted methods of DVT prophylaxis utilizing sequential compression devices and subcutaneous unfractionated heparin may not be adequate to prevent DVT or fatal PE. Methods and Results: 3 morbidly obese patients are described who underwent open Roux-en-y gastric bypass and either had a previous diagnosis of Factor V Leiden or developed thrombosis in the presence of standard prophylaxis. Each was found to have the most common point mutation for Factor V Leiden, R506Q. All 3 patients had prophylactic inferior vena caval filters placed to prevent recurrent PE. Conclusion: The presence of venous thromboembolism either without known risk factors or in the presence of standard perioperative prophylaxis for DVT should warrant a hypercoagulable work-up. Inferior vena caval filter placement is indicated in the presence of a hypercoagulable disorder prior to surgical intervention in the morbidly obese population. The recent literature is reviewed.