Background and objective Cardiovascular disease is the main cause of death in children with chronic kidney disease. Inflammation and endothelial dysfunction are found in the majority of these patients and are factors associated to cardiovascular disease. Flow mediated dilatation (FMD) is a surrogate marker validated for evaluating endothelial dysfunction. Our objective was to identify risk factors associated to endothelial dysfunction in children with chronic kidney disease. Materials and methods Children 2-16 years of age were studied. Clinical information and biochemical variables were gathered, including intact parathyroid hormone (iPTH), interleukins 6 and 1β, high sensitivity C reactive protein (hsCRP), reduced glutathione, nitric oxide, malondialdehyde and homocysteine. FMD was measured, and considered altered if < 7%. Results Included were 129 patients aged 13.1 ± 2.6 years. FMD < 7% was found in 69 (52.7%). Patients with altered FMD had higher levels of triglycerides and hsCRP than those with normal FMD (145.5 vs. 120.0 mg/dL, P = .042, and 1.24 vs. 0.55 U/L, P = .007, respectively), as well as higher frequency of low iPTH (19.1 vs. 4.9%, P = .036). Levels of hsCRP correlated significantly with FMD (Rho = −0.28, P = .003). Patients with low iPTH (OR 4.41, 95% CI 1.13-17.27, P = .033) and increased hsCRP (OR 2.89, 95% CI 1.16-7.17, P = .022) had higher adjusted risk of having FMD < 7%. Conclusions Hypertriglyceridemia, inflammation and low iPTH associated significantly with altered FMD. They are frequent, treatable risk factors for cardiovascular disease.