© 2016, Japanese Society of Nephrology.Background: Cardiovascular disease (CVD) is an important complication of chronic kidney disease (CKD) in children. However, it is not well known when and how cardiovascular alterations start. Methods: This cross-sectional, controlled study consisted of 25 patients and 28 healthy controls. 24-h ambulatory blood pressure monitoring, aortic pulse wave velocity (aPWV), carotid intima-media thickness (cIMT) and carotid distensibility (distensibility coefficient and β stiffness index), and echocardiography were assessed to evaluate CVD. Routine biochemical parameters, fibroblast growth factor-23 (FGF23) and high sensitive C- reactive protein were measured to determine cardiovascular risk factors. Results: Hypertension was found in 12 patients (48 %). Patients had higher FGF23 levels and aPWV-standard deviation score (SDS) as compared to the controls (p = 0.003 and p = 0.002, respectively). Aortic PWV-SDS was predicted by increased daytime systolic blood pressure load (β = 0.512, p = 0.009, R2 = 0.262). Neither cIMT nor distensibility differed between the groups; however, older age and high level of FGF23 were independent predictors of β stiffness index in patients (β = 0.507, p = 0.005, R2 = 0.461 and β = 0.502, p = 0.005, R2 = 0.461, respectively). As compared to controls, patients had worse left ventricular diastolic function [lower E/A ratio p = 0.006) and increased left atrial dimension (p < 0.001)]. Conclusions: Cardiovascular deteriorations appear in children with stage-2 CKD. Good control of BP and decreasing the level of FGF23 may be useful to slow down the progression of cardiovascular complications.