B-type natriuretic peptide (BNP) is a biomarker of cardiovascular disease that is common in adults with chronic kidney disease (CKD). However, in children with CKD, the range and predictive power of BNP concentrations are not known. We aimed to determine the effect of HD on BNP, as well as the prognostic impact of BNP, in end-stage renal disease (ESRD) children undergoing hemodialysis (HD). Thirty-five children with chronic renal failure (16 boys age 12.1 ± 3.7 years) on maintenance HD were included. BNP level was measured, and Doppler echocardiography was performed 30 min before (pre-HD BNP) and 30 min after (post-HD BNP) HD in each patient. An adverse event was defined as all-cause death and heart failure hospitalization. The median pre-HD BNP, the post-HD BNP, and the change in BNP were, respectively, 240 pg/ml (72 to 3346), 318 pg/ml (79 to 3788), and 9 pg/ml (-442 to 1889). Pre-HD BNP concentration was negatively correlated with left ventricular (LV) ejection fraction (r = -0.41, P = 0.018). During a mean follow-up of 39 ± 14 months, 6 patients died, and 3 were hospitalized for heart failure. Using univariate analysis, BNP before and after HD as well as Doppler tissue imaging velocities had a strong graded relationship with adverse events. Cox proportional hazards model demonstrated that pre-HD body weight (P = 0.008), pre-HD BNP (P = 0.011), and post-HD BNP (P = 0.038) remained independent predictors of adverse outcome. Even in case of ESRD, BNP still strongly correlated with LV systolic and diastolic dysfunction and was associated with mortality in HD children.