Aims & Objectives: Capillary refill time is a clinical tool associated with mortality in sepsis. We sought to evaluate the association between prolonged capillary refill time (PCRT) and microvascular and endothelium changes in sepsis Methods: This was a prospective cohort study in children hospitalized in critical care. Microcirculation was measured using perfused boundary region (PBR) on sublingual video microscopy (normal less 2.0 microns- glycocalyx injury), capillary density (CD), capillary blood volume (CBV) and arterio-venous CO2 difference (DCO2). The primary outcome was the association between PCRT and microvascular changes. Results: A total of 132 children (two years; IQR 0.6-12.2) were included. PCRT was associated with elevated PBR (2.21 vs. 2.08 microns; aOR 2.65 95% CI 1.09-6.34; p=0.02), fewer 4-6 micron CD (p=0.03) and an increased percentage of CBV (p=0.01). Patients with hemodynamic incoherence (HI) had more PBR abnormalities (78.4% vs. 60.8%; aOR 2.58 95% CI 1.06-6.29; p=0.03) and the persistence of HI after six hours was associated with higher mortality (16.5% vs. 6.1%; p<0.01). Children with an elevated DCO2 had an abnormal PBR (aOR 1.13 95% CI 1.01-1.26; p=0.03) and a CDs (p<0.05). PCRT predicted an abnormal PBR (AUROC 0.81 95% CI 0.64-0.98; p=0.03) on admission. A normal CRT at 24 hours predicted a shorter hospital stay (aOR 0.96; 95% CI 0.94-0.99; p<0.05).Conclusions: Children with sepsis and PCRT had fewer small capillaries recruited, increased redistribution of blood flow and a higher risk of endothelial glycocalyx degradation. These disorders were associated with hemodynamic incoherence and worse clinical outcomes when the CRT continued to be abnormal 24 hours after admission. Keywords: Mortality, septic shock, perfusion, microcirculation