The objective of this study is to assess the utility of the Guy, S.T.O.N.E., and CROES nephrolithometry scoring systems (SS), and compare the capability of each system to predict percutaneous nephrolithotomy (PNL) outcome in patients with anatomical abnormalities. We retrospectively collected medical records of patients with anatomical abnormalities who underwent PNL for the treatment of renal calculi by experienced surgical teams in four referral centers. All of the patients were graded by a single observer from each department based on preoperative computed tomography images using each SS. Patient demographics and outcomes were compared according to the complexity of the procedure as graded by each scoring system. A total of 137 cases with anatomical abnormalities [horseshoe kidney (n = 46), malrotation (n = 33), kypho and/or scoliosis (n = 31) and ectopic kidney (n = 27)] were assessed retrospectively. The mean stone burden, number, and density were 708.5 mm(2), 1.7, and 791.8 HU, respectively. The mean procedure, fluoroscopy, and hospitalization times were 75.2 +/- 35.3 min, 133.4 +/- 92.3 s, and 3.5 +/- 2.1 days, respectively. Stone-free status was achieved in 106 cases (77.4 %). A total of 17 (13.6 %) complications occurred postoperatively. The mean scores were 2.7, 7.2, and 219.1, for the Guy, S.T.O.N.E., and CROES systems, respectively. CROES score was the independent predictor of PNL success in cases with anatomical abnormalities [p: 0.001, OR 1.01, (95 % CI 1005-1021)]. The CROES scoring system is well correlated with the success of PNL in cases with anatomical abnormalities; the S.T.O.N.E. and Guy scoring systems failed to predict the outcomes of PNL in this specific patient population.