Ischemic preconditioning is a useful tool to fight against reperfusion injury. This phenomenon is very complex and the underlying mechanism has various branches. Every study on ischemic preconditioning helps us to better understand this process. We aimed to investigate the effectiveness of cyclooxygenase-2 (COX-2) on ischemic preconditioning of skin flaps in the rat. A 6 x 3 cm-sized left epigastric artery flap was used and the pedicle was isolated to perform the ischemic preconditioning via microvascular clamp application. The preconditioning protocol was 2 cycles of 15 minutes ischemia and 15 minutes reperfusion periods. Sixty female Wistar rats weighing between 210 and 260 g were used for the experiment. Animals were allocated randomly into 6 groups, each group containing 10 animals. Group 1: Only 6 hours of ischemia was done after the flap elevation, neither ischemic preconditioning nor COX-2 inhibitor was used; Group 2: 6 hours of global ischemia was induced just after the ischemic preconditioning; Group 3: In addition to the same procedures in group 2, 2 doses of COX-2 inhibitor were given before and after the final ischemic insult; Group 4: 6 hours of ischemia was applied to the flap 24 hours after its elevation, no preconditioning or any other interventions were done; Group 5: The same ischemic protocol was used after the flap elevation but the 6 hours of ischemia was performed 24 hours after the preconditioning; Group 6: The same procedures of group 5 were done and in addition, 2 doses of COX-2 inhibitor was given, starting 24 hours after the ischemic preconditioning. All flaps were followed for 1 week then necrotic flap portions were measured and represented as a percentage to the whole flap area. Statistical analyses revealed meaningful differences between groups 2 and 3 (P < 0.05), 2 and 1 (P < 0.05), 5 and 6 (P < 0.05), 5 and 4 (P < 0.05). However, there was no statistical difference between groups 3 and 1 (P > 0.05), 6 and 4 (P > 0.05). As a conclusion, ischemic preconditioning has both early and late protective effects on ischemia-reperfusion injury in the skin flap model. By antagonizing COX-2 receptors the beneficial effects of IP were reversed. This result indicated that COX-2 has a specific role in the mechanism of both early and late effects of ischemic preconditioning in skin flaps.