Background The most widely accepted computed tomography (CT) protocol for diagnosis of acute pyelonephritis (APN) includes at least a pre- and post-contrast scan, which may expose patients to higher doses of ionizing radiation. Purpose To establish the accuracy, reproducibility, and degree of confidence in CT diagnosis of acute pyelonephritis (APN) and urolithiasis using only images obtained during the nephrographic phase. Material and Methods A retrospective study of 100 consecutive patients (88 women; age range, 19–70 years) with clinical and laboratory suspicion of APN and who underwent triphasic abdominal CT scans (non-contrast, nephrographic, and excretory phases) was performed. Two readers first evaluated independently only the nephrographic phase of scans, and, in a second session, the entire study. The diagnostic reference standard was settled by a third experienced radiologist who reviewed all triphasic scans and clinical data. Results The accuracy of only nephrographic phase for diagnosis of APN and urolithiasis was in the range of 90.3–91.78% and 96.27–99.25%, respectively. There was no significant difference in comparison with the triphasic reading (z: −0.4 – 0.2; P = 0.34–0.83). The average degree of confidence for APN also showed no significant variation for both readers ( P = 0.4 and 0.08). Almost perfect inter-observer agreements for the diagnosis of APN (k = 0.86, P < 0.001) and for urolithiasis (k = 0.84, P < 0.001) were observed when considering only the nephrographic phase. Conclusion CT assessment of APN and urolithiasis can be accurately performed using only the late nephrographic phase, with consequent dose reduction.