In clarifying the pathogenesis of inflammatory bowel diseases, a dysregulation of the adaptive immune function was the main focus of research in the last decade. With increasing knowledge of antimicrobial peptides, a primary disturbed barrier function and the system of innate immunity has recently received increasing attention. Contrary to the common understanding of irritable bowel syndrome as a functional disorder, there is first evidence for an involvement of innate immunity for this condition. Peptides with high relevance seem to be the class of human defensins. This article will thus discuss current advances in immunologic research of inflammatory bowel disease and irritable bowel syndrome, focusing on defensins and their possible role as biomarkers of these diseases.