This study has been performed in order to determine the incidence of Aeromonas, Clostridium difficile, Yersinia enterocolitica and VETEC (Verotoxin producing Escherichia coli), in addition to routinely identified pathogens in stool cultures and to discuss necessity and cost effectiveness of the isolation procedures for these uncommon pathogens. Out of 452 stool samples collected from patients admitted to Marmara University Hospital and Haydarpaşa Numune Hospital, the isolation rates were 3% for Shigella, 1.7% for Salmonella, 0.2% for VETEC and, Yersinia enterocolitica and Aeromonas were isolated from none of the stool cultures. However C. difficile was an important pathogen in hospitalised patients with isolation rate of 12.9%.