In this paper we consider recent new data on the pathological features of gluten sensitivity and on the disease-associated antigens, in the context of a multistage hypothesis that we have been developing for the last five years. This incorporates concepts of oral tolerance induction, mucosal T-cell and antibody-mediated injury, and genetic contributions. Until now, there has been complete agreement that the diagnosis of celiac disease must be based on small bowel histology. There are patients with low-grade gluten-sensitive enteropathy, in whom the only morphological abnormality is a high count of intraepithelial lymphocytes (IEL). Some, but not all, also have positive serum IgA anti-endomysium antibody (AEA). With good techniques, in a properly accredited laboratory in a patient suspected on clinical grounds to have celiac disease, a positive serum IgA AEA test (perhaps, alternatively, high-titer anti-transglutaminase by ELISA), is virtually diagnostic of the condition. Our hypothesis of a stepwise pathogenesis of severe gluten-sensitive enteropathy is re-examined in the light of these new data. It is evident that there are at least five different levels at which genetic influences may operate.