Inflammatory bowel diseases are a current and growing public health problem, with a prevalence that appears to be increasing in most countries and cultures. While most research into the triggering phenomenon has focused on the interaction between commensal bacteria and inflammatory bowel disease, enteric fungi may also be important in determining disease susceptibility. Herein we review what is known about enteric fungi and the mechanisms by which they and their dysregulation might be involved in triggering inflammatory diseases of the bowel.