Background: The endothelial glycocalyx (EG) is an important structure that regulates vascular homeostasis. Deep inferior epigastric perforator (DIEP) flap is expected to cause substantial EG breakdown owing to the long procedural duration and ischemia– reperfusion injury. This prospective, randomized, controlled study aimed to compare syndecan-1 levels during sevoflurane-remifentanil and propofol-remifentanil anesthesia in patients who underwent DIEP flap breast reconstruction.Methods: Fifty-one patients were randomized to either sevoflurane (n = 26) or propofol (n = 25) groups. Anesthesia was maintained with remifentanil in combination with either sevoflurane or propofol. The primary endpoint was the concentration of serum syndecan-1 measured at 1 h after surgery.Results: Fifty patients (98.0%) completed the study. Patients in the propofol group had significantly lower levels of syndecan-1 than patients in the sevoflurane group at 1 h after operation (23.8 ± 1.6 vs. 30.9 ± 1.7 ng/ml, respectively; Bonferroni corrected P = 0.012). There were no significant differences between groups in postoperative complications. The postoperative hospital stay was 8.4 ± 2.5 days in the sevoflurane group and 7.4 ± 1.0 days in the propofol group (P = 0.077).Conclusions: Propofol-remifentanil anesthesia resulted in lesser increases in syndecan-1 levels compared to increases with sevoflurane-remifentanil anesthesia in patients who underwent DIEP flap reconstruction. Our results suggest that propofol-remifentanil anesthesia shows protective effects against EG damage during DIEP flap breast reconstruction in contrast to sevoflurane-remifentanil anesthesia.