Deep vein thrombosis (DVT) after total hip or knee arthroplasty is relatively common and is associated with significant morbidity and mortality, presenting a large clinical burden. The objective of this study was to investigate the incidence and risk factors for DVT after total joint arthroplasty. This retrospective review was conducted in a single institution. The patients received postoperative DVT chemoprophylaxis (Fraxiparine or Rivaroxaban), followed by venography to check for DVT on the third to ninth postoperative day. The clinical characteristics were summarized and analyzed using SPSS version 17.0. From March 2010 to July 2013, 963 patients were enrolled in the study. DVT chemoprophylaxis was administered to all of the 963 patients. DVT occurred in 173 subjects (17.96%). Univariate analysis showed that age (P < 0.001), BMI (P < 0.01), cholesterol (P < 0.001), high-density lipoprotein (P < 0.001), apolipoprotein A (P < 0.01), history of tumor (P < 0.05), visual analogue scale (VAS) pain score (P < 0.001), and operative duration (P < 0.05) were significant risk factors for DVT. The incidence of DVT was 17.96% after total joint arthroplasty with prophylactic antithrombotic therapy. Age, BMI, cholesterol, high-density lipoprotein, apolipoprotein A, history of tumor, VAS score, and operative duration were significant risk factors for DVT.