Background/Aims: Proton pump inhibitors (PPIs) and histamine-2 receptor antagonists (H2RAs) are commonly prescribed for stress ulcer prophylaxis (SUP) in critically ill patients. Several studies have suggested that the use of PPIs is a potential risk factor for Clostridium difficile infection (CDI). We compared the incidences of CDI in the PPI group and H2RA group for SUP in critically ill patients. Methods: From August 2005 to July 2012, the incidences of CDI were retrospectively analyzed in patients who were admitted directly to intensive care units and stayed for more than 3 days. SUP-related CDI was defined as a CDI diagnosed during the SUP period. Patient clinical data were analyzed to identify potential risk factors for SUP-related CDI. Results: Of the 1,005 patients enrolled (444 patients received PPI and 561 received H2RA), 38 (3.8%) were diagnosed with SUP-related CDI. The incidence of SUP-related CDI was considerably higher in patients who received PPI than in those who received H2RA (6.7% vs 1.8%). PPI use for SUP (odds ratio [OR], 3.3; confidence interval [CI], 1.5 to 7.1; p=0.003) and diabetes mellitus (OR, 2.3; CI, 1.2 to 4.7; p=0.019) were independent risk factors for SUP-related CDI. Conclusions: PPI therapy is associated with a higher risk of SUP-related CDI than H2RA therapy in critically ill patients.