Objective To study the expressions of hypoxia inducible factor (HIF)-1 and angiopoietin (Ang)-2 in repeated gastrointestinal bleeding due to vascular malformation, and the efficacy of treatment with thalidomide. Methods Twenty-five patients with repeated gastrointestinal bleeding due to vascular malformation confirmed by capsule endoscopy or enteroscopy were collected and 18 subjects without severe diseases were served as controls. Ten patients with gastrointestinal vascular malformation, who received 25 mg of thalidomide 4 times daily for 4 months and were followed up for at least one year, were also enrolled. The serum samples from all participauts were detected for expressions of HIF-1 and Ang-2 using enzyme-linked immunosorbent assay (ELISA).The expressions of HIF-1 and Ang-2 were compared between angiodysplasia group and control group.The expressions of HIF-1 and Ang-2 were comparatively evaluated before and after treatment with thalidomide in treatment group. Results The expressions of HIF-1 and Ang-2 in vascular malformation group [( 113. 84 ± 26. 66 ) ng/ml and ( 652. 11 ± 140. 39) ng/ml, respectively] were significantly higher than that of control group [(43.28±17.30) ng/ml and (265.60±53.88) ng/ml,respectively, P=0. 000]. The expression of HIF-1 was positively associated with that of Ang-2. (r=0. 700, P= 0. 000). There was no difference in expressions of HIF-1 and Ang-2 before and after treatment with thalidomide (P=0. 498 and =0. 136, respectively). However, significant reduction of Ang-2 [(113. 80±73. 60) ng/ml(P=0. 003)] was found in 8 effectively treated patients after thalidomide treatment. Conclusions HIF-1 and Ang-2 might play an important role in the formation of vascular malformation. The extent of Ang-2 reduction after thalidomide treatment may be helpful in evaluating its efficacy or prognosis.