Background: Pharyngitis is one of the most frequently faced pediatric problems with serious complications in primary care. Objective(s): To compare between Integrated Management of Childhood Illness(IMCI) guidelines and traditional management concerning diagnosis and antibiotic prescription for acute pharyngitis in children less than 5 years, as well as to determine validity of IMCI guidelines in diagnosis of acute pharyngitis by comparing their results to throat culture as a golden standard. Methods: A comparative cross-sectional study was conducted in one primary health care center and one unit where IMCI guidelines were implemented; as well as one center and one unit where traditional management of acute pharyngitis was implemented in Zagazig district, on 343 children under five years complaining of sore throat or difficult feeding. About 86 children were randomly selected from each health facility during the period of first of January until end of June 2017. Doctor's clinical diagnosis and antibiotic prescription were reported for all children, while throat swabs were taken from children managed according to IMCI guidelines for bacterial culture. Results: According to IMCI, only 11 % of children were diagnosed as bacterial pharyngitis, antibiotic prescription was significantly lower among those managed according to IMCI compared to traditional methods (11% & 96.5% respectively, P<0.001). However, throat culture revealed that 28.5% of children managed according to IMCI guidelines had positive bacterial growth. Sensitivity of IMCI guidelines to detect bacterial cases of pharyngitis was only 36.7 % and Positive Predictive Value (PPV) was 94.7%, while their specificity to exclude bacterial and detect viral infection was about 99.2% and the Negative Predictive Value (NPV) was 79.7%. Conclusion: Application of IMCI guidelines is considered valuable in prevention of antibiotic abuse.  However, the sensitivity of IMCI guidelines to detect bacterial pharyngitis was 36.7%.