Aim This prospective study aimed to investigate the diagnostic value of serum procalcitonin levels in children with acute pyelonephritis documented by Tc-99m-dimercaptosuccinic acid (DMSA) scintigraphy. Methods We compared the symptoms and laboratory findings of fever, vomiting, abdominal/flank pain, leukocyte count, serum C-reactive protein and procalcitonin levels with the results of the DMSA scan obtained within the first 72 h after referral in children who were diagnosed as having acute pyelonephritis. Thirty-three children (31 female and two male) aged 1-11 years (mean 4.42 years) were enrolled in this prospective study. Results Twenty-one of 33 patients (64%) had positive DMSA scans. On the scans obtained after 6 months, five of 21 patients (23.8%) had renal scars. No correlation was found between clinical and laboratory parameters, alone or combined with each other, and positive DMSA scans. Serum procalcitonin levels were 0.767 +/- 0.64 and 1.23 +/- 1.17 ng (.) ml(-1) in children with normal and positive DMSA scans, respectively. The cut-off value for procalcitonin using receiver operating characteristic analysis was 0.9605 ng (.) ml(-1), while sensitivity and specificity were 86.4% and 36.4%, respectively. However, if the cut-off value was chosen as 2 ng (.) ml(-1), the sensitivity increased to 100% while specificity did not change markedly. Conclusion The serum procalcitonin test, like other commonly used laboratory parameters, e.g. serum C-reactive protein and white blood cell count, was inadequate in distinguishing renal parenchymal involvement in acute febrile urinary tract infections.