Background: Preclinical and clinical studies indicated that endothelial progenitor cells (EPCs) enhanced blood vessel formation in many clinical situations. However, whether transplantation of EPCs would enhance chronic venous thrombus recanalization and resolution is unknown. Methods: Mononuclear cells were isolated from bone marrow of immature rats by density gradient centrifugation, cultured, and then transplanted into inferior vena cava of rats with experimentally induced thrombi. Vascular endothelial growth factor (VEGF), basic fibroblast growth factor (bFGF), messenger RNA (mRNA), and protein expression levels were measured through real-time quantitative polymerase chain reaction and Western blotting of thrombi and adjacent caval walls 14 days following transplantation. Results: Transplantation of bone marrow-derived EPCs led to an increase in VEGF, bFGF, mRNA, and protein expression. In addition, transplantation of bone marrow-derived EPCs also resulted in reduced thrombus size and increased neovascularization in the specimen. Conclusions: Transplanted bone marrow-derived EPCs may be a therapeutic option for treating deep venous thrombosis.