Background: We undertook this study to investigate the presence of C. perfringenes in two groups of diarrheal patients (IBD and non- IBD patients).Methods: A total of 97 stool samples were obtained from patients with gastroenteritis, including 55 (5.85%) from non- IBD patients and 39 (41.5%) from IBD patients. The stool samples were examined for the detection of C. perfringenes and C. difficile after treatment with buffer salin phosphate. The treated samples were cultured on Neomycin Egg Yolk Agar plates supplemented with 5% horse blood and CCFA for isolation of C. perfringens and C. difficile, respectively and incubated at 37oC under anaerobic conditions for 2 days. PCR was done on the extracted DNAs of C. difficile and C. perfringenes colonies for toxin encoding genes tcdA, tcdB and cpe.Results: Out of the 97 stool samples tested, C. perfringenes and C. difficile were detected in 19 (20.2%) and 10 (10.3%) samples, respectively. Two isolates of C. perfringens (2.1%) and 10 (10.3%) isolates of C. difficile were positive for cpe, tcdA, and tcdB toxin encoding genes. No association was found between type of infection in IBD and non-IBD patients groups.Conclusion: Overgrowth of toxigenic strains of C. perfringens beyond C. difficile in diarrheal patients proposes their clinical significance that should be considered by physicians.