Clostridium difficile is a bacteria that causes severe gastrointestinal illness in people. It is the most commonly reported hospital acquired infection in the United States. In this dissertation I explore both medical and environmental risk factors for disease. Epidemiological methods are used to investigate how frequently prescribed gastrointestinal medications affect the microbiome of Clostridium difficile patients. In addition, the roles of toilets and hospital privacy curtains are explored as potential environmental sources of patient infection.