Abstract. Aim: The aim of this study was to assess the expression of calprotectin in the stools of neonates with hypoxic ischemic encephalopathy (HIE). Method: Fecal calprotectin was measured at 2 and 10 postnatal days in full-term neonates with HIE and was compared to healthy matching controls. Results: Forty-two infants were studied; 21 suffered from HIE and 21 matching controls. Initial and 10-days-postnatal concentrations of calprotectin were significantly greater in patients compared to controls; patients with severe HIE had the highest concentrations. Initial stool calprotectin had 100% sensitivity and 100% specificity as a marker in patients with different grades of HIE having a cut off value of 355 ug/g. Multiple regression analysis revealed that the most determinant factor for fecal calprotectin at 10 days was the start of oral feeding. Conclusion: Fecal calprotectin is significantly increased in neonates with HIE; its concentration correlates with the severity of the disease. Additionally, start of feeding is the most determinant factor for calprotectin expression at 10 days in this population. Further studies are recommended to assess the utility of calprotectin in determining the best time to start enteral feeding and to correlate its concentration with other laboratory and hemodynamic markers of gut ischemia.