ABSTRACT Objectives Measurements of stone features may vary according to the non-contrast computed tomography (NCCT) technique. Using magnified bone window is the most accurate method to measure urinary stones. Possible differences between stone measurements in different NCCT windows have not been evaluated in stones located in the kidney. The aim of this study is to compare measurements of kidney stone features between NCCT bone and soft tissue windows in patients submitted to retrograde intrarenal surgery (RIRS). Materials and Methods Preoperative and 90th postoperative day NCCT were performed in 92 consecutive symptomatic adult patients (115 renal units) with kidney stones between 5 mm to 20 mm (< 15 mm in the lower calyx) treated by RIRS. NCCT were evaluated in the magnified bone window and soft tissue window in three axes in a different time by a single radiologist blinded for the measurements of the NCCT other method. Results Stone largest size (7.92±3.81 vs. 9.13±4.08; mm), volume (435.5±472.7 vs. 683.1±665.0; mm3) and density (989.4±330.2 vs. 893.0±324.6; HU) differed between bone and soft-tissue windows, respectively (p<0.0001) 5.2% of the renal units (6/115) were reclassified from residual fragments > 2 mm on soft tissue window to 0-2 mm on bone window. Conclusion Kidney stone measurements vary according to NCCT window. Measurements in soft tissue window NCCT of stone diameter and volume are larger and stone density is lesser than in bone window. These differences may have impact on clinical decisions.