Knowledge of the pyelocaliceal system anatomy is essential for the safe and successful performance of endourologic procedures. The purpose of this study was to provide a better understanding of the full three-dimensional pyelocaliceal system anatomy. Morphometric parameters of the three-dimensional reconstructions of computed tomography intravenous urography scans (n = 25 scans) were analyzed. Both kidneys were divided into three equal-sized segments (US: upper segment, MS: mid segment, LS: lower segment). Infundibular length (IL), infundibular width (IW), the number of calyces, and the transverse orientation in hours of a clock of each calyx as well as the dimension of the pyelum were determined. The mean upper IL (n = 92) was longer than the middle (n = 154) and lower IL (n = 112) (30.6 ± 7.9mm vs. 16.4 ± 7.7mm vs. 16.0 ± 6.0mm, respectively; P = < 0.0001). IW was significantly smaller in the MS [3.7 ± 1.9mm], followed by the US [4.6 ± 1.9mm], and the LS [4.9 ± 2.2] in the increasing order. No correlation was found between IL and IW (Pearson correlation coefficient = 0.1). The US calyces were predominantly orientated lateral (8-10 o'clock: 44.5%) and medial (2-4 o'clock: 30.5%), in the MS lateral (8-10 o'clock: 87.6%) and anterolateral in the LS (9-12 o'clock: 67.9%). 74% of the kidneys consisted of 6-8 calyces (mean 7.2 ± 1.4, range 4-10), with the majority of the calyces in the MS (3.1 ± 0.8) followed by the LS (2.24 ± 0.8), and US (1.8 ± 0.7). There were no statistical differences between the right and left kidneys in terms of IL (P = 0.112) and number of calyces (P = 0.685). Anatomic differences between the three segments of the pyelocaliceal system in terms of IL, IW, calyces number, and orientation are seen and should be considered when performing an endourologic procedure.