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Abstract: Objective To investigate the incidence and clinical features of non-Clostridium difficile (C.difficile) associated nosocomial diarrhea in intensive care unit (ICU) caused by Klebsiella oxytoca and Clostridium perfringens. Methods The faeces of 102 patients with non-C.difficile associated nosocomial diarrhea in ICU of West China Hospital, were collected during April to November, 2012. The target bacterial genes were detected by PCR amplification and sequencing, including toxic gene pehX of Klebsiella oxytoca, species-specific 16S rRNA gene and toxic gene cpa and cpe of Clostridium perfringens, species-specific 16S rRNA gene with mapA and toxic gene hipO of Campylobacter jejuni. Clinical features of the patients with positive results were summarized. Results Among 102 patients with non-C.difficile associated nosocomial diarrhea, 4 patients (3.9%) were detected with toxic Klebsiella oxytoca while 4 patients (3.9%) were detected with toxic Clostridium perfringens. No toxic Campylobacter jejuni was detected. Most of the patients had severe underlying diseases and poor final outcome, accepted potent antibiotics which disturbed intestinal flora obviously.. Conclusion Non-C.difficile associated nosocomial diarrhea in ICU caused by Klebsiella oxytoca is and Clostridium perfringens is associated with severe diseases and poor outcome, but the incidence in our hospital is relatively low in our hospital.