A better understanding of the pathophysiology of ischaemia-reperfusion injury and a possible treatment for it, is of great importance. The deep inferior epigastric perforator (DIEP) flap is an innovative, clinical model of ischaemia-reperfusion. There has been an ongoing interest in the health benefits and medical applications of antioxidants. We hypothesised that during ischaemia-reperfusion, specific antioxidants are depleted. Seventeen DIEP flaps were performed in 15 patients undergoing breast reconstruction. In each free flap, 3-mm skin biopsies were taken from the DIEP flap at four different time points during and after surgery. In those tissue biopsies, concentrations of the antioxidants vitamin E, glutathione (GSH) and uric acid and total antioxidant capacity (TEAC) were measured. Unexpectedly, no immediate change was observed in GSH concentrations during ischaemia-reperfusion. Uric acid concentrations were significantly increased at all time points following reperfusion. Vitamin E concentrations also showed a significant incline 30min and 1h after reperfusion. However, 1h after reperfusion, a significant decrease in total hydrophilic antioxidant capacity (TEAC) was seen. In the next hour, this capacity recovered. During ischaemia-reperfusion, a deficiency in hydrophilic antioxidant capacity develops. This is a potential cause for the development of ischaemia-reperfusion injury by reactive oxygen species. This clinical trial is registered on Clinical Trials: http://www.clinicaltrials.gov/. Trial registry name: The DIEP-flap as a model of ischaemia-reperfusion. Registration identification number (NCT): 00482469.