Gastroenterologists frequently treat patients with complex illnesses such as chronic hepatitis C infections and inflammatory bowel disease (IBD). Occasionally, a patient will present with these two diseases which behave very differently and the treatment for one may potentially exacerbate the other. The purpose of this article is to review the current literature regarding hepatitis C virus therapy in the setting of IBD as well as the effects of common IBD therapies on the hepatitis C virus. Based on limited data, anti-viral therapy is probably safe in patients with well-controlled IBD, but there might be a risk of causing new onset of IBD. Also, it does not appear that the commonly used medications for IBD have much of an effect on the hepatitis C virus (HCV) or its course.