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Clostridium difficile is the leading cause of healthcare-associated diarrhea in Western and industrialized countries. This work will provide you with an overview about Clostridium difficile and an investigation of the prevalence of C.difficile colonization and its role in antibiotic associated diarrhea among patients in the hospital setting at Theodor Bilharz Research Institute (TBRI), Cairo, Egypt. This work also aimed at developing a multi step algorithm that can provide a specific and cost- effective approach to the laboratory detection of C.difficile from faecal specimens.