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Background: Antibiotic-associated diarrhea (AAD) is a major nosocomial as well as a community health problem. Clostridium difficile toxins (CDT) can be detected in only 10-25% of patients with AAD. The role of Clostridium perfringens enterotoxin A (CPEnt) as a cause of AAD remains to be elucidated. We, therefore, prospectively investigated the prevalences of both CPEnt and CDT in stool samples of patients with AAD., Materials and Methods: A total of 693 stool samples consecutively submitted to our department from patients with AAD were screened for CDT and CPEnt using commercially available enzyme-linked immunoassays (ELISA). C. difficile and C. perfringens were detected by standard culture techniques. In addition, samples being CPEnt positive and/ or harboring C. perfringens were screened for the CPEnt gene by duplex PCR., Results: CDT was detected in 79 (11.4%) of 693 stool samples. Of these, 49 (62.0%) harbored C. difficile. In one (0.14%) of 693 samples, CPEnt could be detected by ELISA. This respective CPEnt-positive stool sample also harbored C. perfringens. 147 (21.2%) of all stool samples were culture positive for C. perfringens. We did not detect samples positive for both CPEnt and CDT. In five (3.4%) of 147 C. perfringens isolates, the CPEnt gene could be detected by duplex PCR. PCR was positive in two (40%) of the five stool samples harboring CPEnt gene-positive C. perfringens isolates., Conclusion: The present prospective study revealed a prevalence of CDT of 11.4%, whereas the prevalence of CPEnt was less than 1%. Routine screening of stool samples for CPEnt does not appear to be justified in patients with AAD.