The purpose of this study was to evaluate the effects of systemic and intra-arterial application of heparin by measuring tissue levels of inflammatory cytokines. Twenty-one adult male Wistar albino rats were divided into three groups (Group A, B and C). All the rats had undergone ligation of the right femoral artery with 4-0 silk suture to induce limb ischemia. Group A was the control group. In Group B, unfractionated heparin of 1500 U/kg/day was given through the tail vein for 10 days, the same dose was given to distal part of ligated right femoral artery for 10 days in Group C. On the 3rd, 5th, and 10th days, biopsies were taken from rectus femoris muscle on the ischemic extremities. Tumor necrosis factor-α, interleukin-1β, and vascular cell adhesion molecule levels in muscle tissue were measured by a standard enzyme-linked immunoabsorbent assay method. An increase in tumor necrosis factor-α level was found in all three groups throughout the duration of the experiment. The increase in Group C was statistically significant as compared with the other groups. The significant increases that occurred in tumor necrosis factor-α level as a result of intra-arterial application of heparin can be postulated to be one of the results of angiogenesis induced by the heparin in ischemic extremities. This might delay the formation of a necrosis in ischemic extremities, depending on the increased angiogenesis response by means of intra-arterial heparin application and may result in extended vitality of an extremity.