Objective: To establish a rat model of chronic hindlimb ischemia and compare it with its acute hindlimb ischemia model, and then analyze the differences in blood perfusion and gene expressions between the two models. Methods: Forty SD rats were equally randomized into two groups to create the chronic (procedure: in the right hindlimb of the rat, an anticoagulant silicon tube was inserted into the femoral artery and fixed in position after the ligation and division of the branches of the iliacofemoral artery) and acute (procedure: in the right hindlimb of the rat, the femoral artery was ligated and excised after the ligation and division of the branches of the iliacofemoral artery) hindlimb ischemia models. The blood perfusion of the hindlimbs was measured using Laser Doppler perfusion imaging before and during the following four weeks after operation. The gene expression of hypoxia-inducible factor 1α (HIF-1α) and vascular endothelial growth factor (VEGF) 24 hours after operation in adductor femoris muscle of the ischemic limb was detected by Real-time PCR. Results: Twenty-four hours after operation, the expression levels of both HIF-1α and VEGF in adductor femoris muscle of the ischemic limb of the acute ischemia group were significantly higher than those of the chronic ischemia group (both P＜0.05). In acute ischemia group, the blood perfusion of the pathological limb dropped to 24% of the contralateral healthy limb but restored rapidly, which reached and stabilized at 82% after 28 days. In chronic ischemia group, the blood perfusion decreased gradually to the minimum level (48%), and then recovered slowly to the highest level (67%) at 28 days after operation. The blood perfusion levels at each observation time point between the two groups were significantly different (all P＜0.05). Conclusions: The pathological characteristics and gene expression profiles of rat model of chronic hindlimb ischemia is different than that of the acute one, and the chronic model is more clinically relevant to the pathological process of critical limb ischemia.