Aims & Objectives: The compromise of microcirculation in children with sepsis is not recognized. We do not know the changes in microcirculation with the use of inodilators. To evaluate the functional capillary density [CD], blood flow, and endothelial glycocalyx changes associated with the use of milrinone. Methods: Prospective cohort study from February 2022–January 2023 (University hospital in Bogotá, Colombia). Sublingual video microscopy was used to evaluate 4-6 micron CD, microvascular flow and perfused boundary region (inverse parameter of glycocalyx thickness–abnormal if > 2.0 microns). The primary outcome was the association between microcirculation and endothelial glycocalyx changes related to the use of milrinone. Results: A total of 140 children (median age of two years [IQR 0.58-12.1]) were included. Twenty-four hours after admission, these patients with milrinone maintained functional capillary density (p<0.01) and capillary recruitment capacity (p=0.04) with no changes in capillary blood volume. Children under two years old who received milrinone had better 4-6 micron CD than older children (OR 0.33; 95% CI 0.12-0.89; p=0.02) and less endothelial glycocalyx degradation (aOR 0.34 95% CI 0.11-0.99; p=0.04). These changes persisted despite elevated ferritin and C-reactive protein (CRP) (aOR 0.41; 95% CI 0.18-0.93; p=0.03). The patients who died had the highest PBR levels (p=0.04).Conclusions: In children with sepsis, we noted that milrinone infusions were found to maintain functional capillary density and capillary recruitment capacity and had less endothelial glycocalyx degradation 24 hours after administration. These changes were present despite the inflammatory response and were more significant in those under two years of age. Keywords: glycocalyx, endothelium, septic shock, microcirculation, glycocalyx, endothelium, septic shock, children, microcirculation