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In this paper, we present an automatic renal cortex segmentation approach using the implicit shape registration and novel multiple surfaces graph search. The proposed approach is based on a hierarchy system. First, the whole kidney is roughly initialized using an implicit shape registration method, with the shapes embedded in the space of Euclidean distance functions. Second, the outer and inner surfaces of renal cortex are extracted utilizing multiple surfaces graph searching, which is extended to allow for varying sampling distances and physical constraints to better separate the renal cortex and renal column. Third, a renal cortex refining procedure is applied to detect and reduce incorrect segmentation pixels around the renal pelvis, further improving the segmentation accuracy. The method was evaluated on 17 clinical computed tomography scans using the leave-one-out strategy with five metrics: Dice similarity coefficient (DSC), volumetric overlap error (OE), signed relative volume difference (SVD), average symmetric surface distance (Davg), and average symmetric rms surface distance (Drms). The experimental results of DSC, OE, SVD, Davg, and Drms were 90.50%±1.19%, 4.38% ±3.93%, 2.37% ±1.72%, 0.14 mm ±0.09 mm , and 0.80 mm ±0.64 mm, respectively. The results showed the feasibility, efficiency, and robustness of the proposed method.