Objective To compare the value of modified Alvarado score and MSCT in the diagnosis of acute appendicitis. Methods 316 cases with suspected acute appendicitis on the going MSCT were included. The modified Alvarado score were retrospectively analyzed. The accuracy, sensitivity, specificity, positive predictive value and negative predictive value of MSCT in the diagnosis of acute appendicitis were estimated. The patients were divided into low, median, high groups according to the modified Alvarado score. The difference of the modified Alvarado score between patients with and without acute appendicitis and the distribution of acute appendicitis among different score groups were analyzed using χ2-test. Results Of 316 suspected cases, 102 (69.9%) were proven by surgical operation, 44 were cured by conventional medical management, and 170 were confirmed to be without acute appendicitis. The number of patients with low, median, high modified Alvarado score were 30(9.5%), 104(32.9%) and 182(57.6%). The accuracy of MSCT was 97.5%, while the sensitivity, specificity, positive predictive value and negative predictive value were 98.6%, 96.5%, 96.0% and 98.8%.The modified Alvarado score of patients with acute appendicitis was higher than that of patients without acute appendicitis(P<0.001). The diagnostic accuracy of modified Alvarado score in women was lower than men in all groups. Conclusion The performance of MSCT was better than that of modified Alvarado score for the diagnosis of acute appendicitis. However, Modified Alvarado score could be used for patient stratification.