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The purpose of this study was to compare the results of the Alvarado and Pediatric Appendicitis Score (PAS) scoring systems and to establish which one is more reliable in setting the diagnosis of acute appendicitis in children.All children operated on because of acute appendicitis from October 2011 to May 2013 were enrolled in this prospective study. Both clinical scoring systems have been compared over the same patients, and cutoff values were determined by the receiver operating characteristic curve analysis.A total of 311 patients were included in the study, and 265 (85.2%) of them had acute appendicitis. Mean Alvarado score for patients with appendicitis was 8.2 and 6.7 for those without (P < 0.001). Mean PAS for patients with appendicitis was of 7.8 and 6.6 for those without (P < 0.001). Based on the ROC curve analysis, a cutoff value for both scoring systems was 7. In patients with acute appendicitis and Alvarado score of 7 or higher, the correct diagnosis would have been set in 236 patients (sensitivity, 89%; specificity, 59%; positive predictive value, 93.1%), whereas in patients with acute appendicitis and a PAS of 7 or higher, the correct diagnosis would have been set in 228 patients (sensitivity, 86%; specificity, 50%; positive predictive value, 90.1%). No significant difference was found in sensitivity and specificity between the observed scoring systems.Both scoring systems can be of assistance in setting the diagnosis of acute appendicitis, but none has adequate predictive values in assessing acute appendicitis and none can be used as an exclusive standard in setting the diagnosis of acute appendicitis in children. The final decision still remaines on the opinion of an expert pediatric surgeon.