Background Renal hypoxia is considered a final pathway in the progression of chronic kidney disease (CKD). Blood-oxygenlevel-dependent magnetic resonance imaging (BOLD-MRI) has shown merit for evaluating renal oxygenation in adults.Objective To investigate renal cortical and medullary R2* values by CKD stage and by renal function index in children with chronic kidney disease. Materials and methods Twenty-one children with CKD Stage 1-3, 16 children with CKD Stage 4-5, and 6 healthy volunteers underwent a renal MRI using multigradient recalled-echo sequence with 16 echoes. We measured the R2* values of the renal cortex and medulla on BOLD-MRI. Results The cortical R2* value was ranked as CKD Stage 4-5 > CKD Stage 1-3 > healthy controls, and the medullary R2* value was ranked as CKD Stage 4-5 > CKD Stage 1-3. There was no significant difference in the medullary R2* value between CKD Stage 1-3 patients and the healthy controls. There was a positive correlation between the R2* values in the renal cortex (r=0.73) and medulla (r=0.89), and the serum creatinine level (P<0.001), and the renal cortical and medullary R2* values were negatively correlated with the estimated glomerular filtration rate (r=-0.71 and r=-0.89, respectively; P<0.001). Conclusion BOLD-MRI might contribute to noninvasive assessment of renal oxygenation in children with CKD in vivo but it did not reflect renal function in our sample.