The invention includes novel methodology for diagnosing immunologic food or drug sensitivities. The method for diagnosing food sensitivities includes using diagnoses of other related disorders, such as microscopic colitis or other chronic immunologic/autoimmune syndromes, chronic diarrhea, irritable bowel syndrome, and hepatitis C and other hepatic diseases, Crohn's disease, alcoholism, and other idiopathic neuropsychiatric and neurologic disorders, as indicators in the diagnosis of the food sensitivity. Additionally, failure to respond to or a relapse after treatment for microscopic colitis with bismuth subsalicylate is disclosed by the present invention as being a further indicator in the diagnosis of immunologic food sensitivity. Finally, the presence of certain HLA-DQ alleles, particularly HLA-DQ1,3; -DQ1,7; -DQ1,8; and -DQ1,9, HLA-DQ1,1, and at least two subtypes of the HLA-DQ1 allele identified by molecular analysis as HLA-DQB1*0501 and HLA-DQB1*0602, as indicators in diagnosing immunologic food sensitivity, particularly gluten sensitivity or celiac sprue, and in diagnosing the related disease of microscopic colitis and other autoimmune disorders is also disclosed by the invention. A method for food sensitivity panel testing (for sensitivities other than gluten sensitivity) by detecting IgA antibodies in serum is also disclosed. A method for testing stool samples for the presence of particular antibodies, which is more sensitive and less invasive than prior art testing methods, is also disclosed for diagnosing immunologic food sensitivities. These methods of diagnosis may be used alone or in combination to further enhance the accuracy of diagnosis.