The intraoperative irrigation of the surgical site with antiseptics in abdominal surgery has been previously proposed as a way to reduce the rate of surgical site infections. Polihexanide achieves the best results in vitro. We hypothesized that the application of this antiseptic to the surgical site throughout the whole surgical procedure is superior to its common use solely at the end of surgery.In this pilot trial, we compared the long and short intraoperative application of polihexanide in elective abdominal surgery. In the “long” group, the subcutaneous tissue of the incisional wound was kept in contact with 0.04% polihexanide throughout the procedure. In the “short” group, wounds were merely irrigated with polihexanide immediately prior to skin closure.Forty-eight patients in the “long” group and 49 in the “short” group could be analysed. Surgical site infections occurred in 18.8% of the “long” and 20.4% of the “short” group patients. The adjusted infection rates were 19.8% and 16.1%, respectively.Crude and adjusted SSI rates of both groups were nearly similar, so we concluded that this pilot data showed no measurable difference and a trial with larger sample size would be needed to determine a difference.