The following was posted by Kemp Randolph on the Celiac Listserv news group firstname.lastname@example.org:
My non-professional stab at the difference between intolerance and allergy then. Both can lead to intestinal damage. Theres a table in Marshs book showing that --page 155 , figure 6.13. Type 3 damage (flat destructive ) can occur from milk, soy, egg.... as well as celiac disease.
The reaction to an intolerance seems to be that the substance is not digested. The immune part of the response involves only the circulating immunoglobins IgA, maybe IgG and related immune cells, receptors.
The immune reaction to an allergy involves IgE. The substance may still be digested, but there may be allergic responses elsewhere outside the gut.
Apple belly celiac disease is an intolerance. The problems elsewhere in the body, except for cancer, are related to nutritional deficiencies. The link to other autoimmune diseases is statistical genetics when two (or more) genes for each of two conditions are close together.
For more information see the Allergy vs. Intolerance page.