Background: Clostridium difficile-associated diarrhea (CDAD) is a potentially preventable and often troublesome gastrointestinal complication after cardiac surgery. Methods: A retrospective study was performed of 8,405 cardiac surgery patients at two institutions between January 1997 and August 2004. Preoperative cardiac risk factors, perioperative factors including blood product transfusion, antibiotic utilization, and postoperative morbidity and mortality were recorded. Univariate and multivariate analyses were performed comparing C difficile patients with a control group matched by date of surgery and institution. Results: Sixty-six of the 8,405 patients identified with toxin-positive CDAD produced an overall incidence of 0.79% (0.70% at institution A and 1.09% at institution B), with a peak overall incidence of 5.45% in June 2003. Independent prognostic factors for CDAD by multivariate analysis included advancing age (odds ratio [OR] 1.028, 95% confidence interval [CI]: 1.001 to 1.056; p = 0.034), female sex (OR 2.026, 95% CI: 1.102 to 3.722; p = 0.022), blood product transfusion (OR 3.277, 95% CI: 1.292 to 8.311; p = 0.006), and increasing cumulative days of antibiotic administration (OR 1.046, 95% CI: 1.014 to 1.080; p = 0.004). There were no differences in the proportion of fluoroquinolones, cephalosporins, or penicillin derivatives administered between groups. The diagnosis of CDAD was associated with a greater median length of mechanical ventilation (25 hours versus 12 hours, p < 0.001), longer intensive care unit stay (5 days versus 2 days, p < 0.001), and extended hospital stay (21 days versus 7 days, p < 0.001), with no difference in 30-day mortality (7.6% versus 9.5%, p = 0.80). Conclusions: Although the overall incidence of CDAD was low, alteration in transfusion practices and antibiotic utilization may impact the development of CDAD among cardiac surgical patients.