Background: Clostridium difficile infection (CDI) is a leading cause of healthcare-associated infections accounting for significant disease burden and mortality. The clinical spectrum of C difficile ranges from asymptomatic colonization to toxic megacolon and fulminant colitis. Objective: The present study aimed to evaluate the sensitivity and specificity of PCR in comparison with toxigenic culture for diagnosis of antibiotic-associated diarrhea due to Cl difficile infection. Materials and methods: This comparative study was conducted on 80 patients with antibiotic associated diarrhea (AAD). Toxigenic culture (TC) was done for detection of toxigenic Cl difficile and, PCR assay was done for detection of tcdA and tcdB genes and results of both methods were compared. Results: Out of 80 diarrhea patients included in the study, 12 (15%) were positive and 68 (85%) were negative for toxigenic culture. Out of 80 diarrhea patients included in the study, 32 (40%) were positive and 48 (60%) were negative for PCR. The sensitivity, specificity, PPV and NPV of PCR in diagnosis of Cl difficile infection were 100%, 70%, 61.5% and 100% respectively. Also, there was a highly significant difference between positive and negative results as detected by PCR. Conclusion: we can conclude that PCR is a highly sensitive method (100% sensitivity) as compared to TC in diagnosis of antibiotic-associated diarrhea due Cl difficile infection.