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Purpose: The purpose of the study was to explore the application of blood oxygenation level-dependent functional magnetic resonance imaging (BOLD-MRI) in classification of chronic kidney disease (CKD).Methods: Twenty-nine cases with CKD and 27 healthy volunteers underwent renal BOLD-MRI. Cases of CKD were divided into two groups according to the estimated glomerular filtration rate (eGFR). The R2* values were measured in renal cortex and medulla, respectively. The difference of R2* between renal cortex and medulla was compared, and the correlations of R2* value in renal cortex and medulla with eGFR were analyzed.Results: Twenty-nine cases of CKD were divided into two groups, with 13 cases of mild renal impairment and 16 cases of moderate to severe renal impairment. In the control and mild renal impairment group, the R2* of renal cortex was significantly lower than that of medulla (P < 0.001). In the control group, mild renal impairment and moderate to severe renal impairment group, the R2* value of cortex increased, while the R2* value of medulla gradually decreased. The eGFR of patients was positively correlated with R2* of medulla (r = 0.81, P < 0.001), while displayed no correlation with R2* of cortex (r = − 0.32, P > 0.05). When the threshold of R2* of medulla was set at 28.4 Hz, the sensitivity and specificity to distinguish normal and mild renal impairment group were 92.31% and 85.19%, respectively.Conclusion: The change of blood oxygen in renal cortex and medulla could be detected with BOLD-MRI, so as to evaluate the renal function and anoxic injury of CKD. [ABSTRACT FROM AUTHOR]