Diarrhea is a common complication of hematopoietic stem cell transplant (HSCT) due to multiple etiologies, including toxicity from the conditioning regimen and Clostridium difficile (C. difficile) infection. We hypothesized that C. difficile infection is uncommon in recipients of autologous HSCT (auto-HSCT) and testing for C. difficile is over utilized at our institution. We performed a retrospective, single center analysis of the use of polymerase chain reaction (PCR) testing for C. difficile among adult auto-HSCT recipients in the first 45 days post-procedure. Patients were identified by cross referencing the existing list of patients who had an auto-HSCT between May 2011 and May 2014 with the Premier SafetySurveillor® list of C. difficile PCR tests conducted in patients during the same time period. Among the 160 patients identified, the incidence of C. difficile infection was 5.0% with nearly three-quarters of auto-HSCT patients being tested. We further reviewed C. difficile PCR positive patients for risk factors according to Infectious Diseases Society of America (IDSA) guidelines for C. difficile infection. Based upon assessment of risk factors in patients who tested positive for C. difficile infection, we recommend additional study to evaluate for the need for antimicrobial prophylaxis with fluoroquinolones during the neutropenic post-transplant period as well as proton pump inhibitor (PPI) therapy in this patient population. Limiting the use of these agents could be a method to decrease C. difficile risk factors; therefore, potentially decreasing PCR testing and C. difficile infection.