<b><i>Purpose:</i></b> Low-dose computer tomography (NCCT) is the standard imaging modality for patients with acute flank pain with a suspicion of urolithiasis. The stone size is usually measured 2D by a radiologist. We compared 3D stone measurement using different windows to the 2D measurement and evaluated the clinical impact on ureterorenoscopic stone removal (URS). <b><i>Methods:</i></b> One hundred sixty-four patients (201 stones) with a preoperative NCCT, following a URS within 4 weeks, were included in this study. Stone location, number and size of stones, operating time, and laser lithotripsy were documented. Stones were measured in 3D using bone and soft tissue window. The maximum diameter was compared to the radiological report. The U test, Kruskal-Wallis, and regression were used for statistical analyses. <b><i>Results:</i></b> Almost two-thirds (64.68%; 130 stones) of stone measurements in 3D with the bone window were lower than the radiologist reports in 2D. One-third (34.83%; 70 stones) of stone measurements were higher and 0.5% (1 stone) reported the same size. Using the 3D soft tissue window, 81.09% (163 stones), 17.91% (37 stones), and 1% (2 stones) of stones were measured bigger, smaller, or had the same measurement results, respectively. In the clinical setting, we could calculate a cutoff for laser lithotripsy at a maximum stone diameter of 5.70 mm (<i>p</i> &#x3c; 0.01) with the 3D and 6.01 mm with the 2D measurements, respectively, and found a significant correlation between maximum stone diameter and operating time (<i>p</i> &#x3c; 0.01) and number of stones and operating time (<i>p</i> &#x3c; 0.01 with and <i>p</i> = 0.02 without laser). <b><i>Conclusion:</i></b> 3D stone measurement with bone window seems to be more accurate than 2D measurement, but 2D is sufficient for planning stone treatment.