Perinatal hypoxia results in poor circulation in internal organs, causing damage to the intestinal mucosa. Here, we aimed to evaluate the role of endothelial vasoconstrictor function in the formation of the intestinal mucous barrier in low-birth-weight neonates with hypoxicischemic encephalopathy (HIE). We comparatively analysed the concentrations of specific intestinal protective markers, i.e., serum mucin 2 (MUC2), serum intestinal trefoil factor (ITF), and faecal human β-defensin 2 (HBD2), and a marker of endothelial activity, i.e., serum endothelin-1 (ET-1), in early of postnatal life in 8 infants with moderate/severe HIE (group 1), 14 neonates with mild HIE (group 2), and 20 control infants using standard enzyme-linked immunosorbent assays. Markers of intestinal mucosa activity were not differentially expressed between infants in groups 1 and 2. Mean total concentrations of ITF and HBD2 were higher in groups 1 and 2 than in the control group (p < 0.05). In contrast, MUC2 concentrations were lower in infants of groups 1 and 2 than in the control infants. ET-1 expression was higher in group 2 than in group 1 and the control group on days 1-3 (p < 0.05). Spearman's rank-order correlation analysis showed that there were no significant relationships of ET-1 with MUC2 and HBD2. However, there was a significant negative correlation between ET-1 and ITF in group 1 infants. High serum ITF and faeces HBD2 levels accompanied low blood concentrations of MUC2, reflecting the depletion of Goblet cell function in response to hypoperfusion in low-birth-weight infants with HIE.