Expression of class II antigens on human intestinal epithelial cells was assessed using a sensitive avidinbiotin-peroxidase technique. HLA-DR was present predominantly in the normal small bowel with diminished but evident expression in the colon. HLA-DP staining was less prominent, and HLA-DQ was absent. In inflammatory bowel disease the expression of both HLA-DR and HLA-DP was increased, but that for HLA-DQ remained absent, suggesting an inherent defect in the ability of intestinal epithelial cells to express HLA-DQ. In related experiments, an interferon gamma-treated malignant epithelial cell line T84 also failed to stain for HLA-DQ and HLA-DP despite the presence of HLA-DR. Isolated RNAs for all three subclasses of HLA-D were detectable by slot-blot analysis, suggesting that the lack of HLA-DQ expression relates to posttranscriptional defects in intestinal epithelium. These and other differences with conventional class II antigen-positive accessory cells (macrophages/B cells) may help to explain the unique properties of intestinal epithelial cells as antigen-presenting cells.