"Food-induced enteropathy: Cow's milk proteins and soy proteins can cause an uncommon syndrome of chronic diarrhea, weight loss, and failure to thrive, similar to that appearing in celiac disease. Vomiting is present in up to two thirds of patients. Small bowel biopsy shows an enteropathy of variable degrees with villous hypotrophy. Total mucosal atrophy, histologically indistinguishable from celiac disease, is a frequent finding."
eMedicine: Protein Intolerance

 

"Up to 20% of celiacs will continue to experience loose or watery stools even after going on a GF diet. Sometimes this is due to inadvertent gluten in the diet, but a recent study at Dr. Fine's medical center showed that in these cases other diseases epidemiologically associated with celiac disease are present.[7] These include microscopic colitis, exocrine pancreatic insufficiency, lactose intolerance, selective IgA deficiency, hypo- or hyperthyroidism, and Type I diabetes mellitus. When diarrhea continues after beginning a GF diet, a search for these associated diseases or others should be undertaken and treated if found." From Celiac.com
 

Dr. Nelson - see Other tests to consider if not Celiac Disease

 
Parasitic and bacterial infections in individuals with gastrointestinal symptoms
 From Nutritional Healing 

 
WebMD on Habba Syndrome

 

PubMed Abstracts:

Symposium 1: Joint BAPEN and British Society of Gastroenterology Symposium on 'Coeliac disease: basics and controversies' Coeliac disease: optimising the management of patients with persisting symptoms?
PMID: 19555521 June 2009

Bovine milk intolerance in celiac disease is related to IgA reactivity to alpha- and beta-caseins.
PMID: 19268534  June 2009


Conclusion: Celiac disease is the most common cause of malabsorption syndrome in both adults and children. These people harbor significantly more pathogenic parasites and are more frequently colonized with harmless commensals as compared to healthy controls. Intestinal coccidia are associated with malabsorption syndrome, particularly in malnourished children.
Parasites in Patients with Malabsorption Syndrome: A Clinical Study in Children and Adults.
PMID: 17763958 Aug 2007

[Focal villous atrophy of the duodenum in children who have outgrown cow's milk allergy. Chromoendoscopy and magnification endoscopy evaluation]
PMID: 17625280  June 2007


Gluten exposure was the most common cause of NRCD (36%), followed by irritable bowel syndrome (22%), refractory CD (10%), lactose intolerance (8%), and microscopic colitis (6%).
Etiologies and predictors of diagnosis in nonresponsive celiac disease.  PMID: 17382600   April 2007

Pancreatic exocrine insufficiency with steatorrhea is a major consequence of pancreatic diseases (eg, chronic pancreatitis, cystic fibrosis, severe acute necrotizing pancreatitis, pancreatic cancer), extrapancreatic diseases such as celiac disease and Crohn's disease, and gastrointestinal and pancreatic surgical resection. Recognition of this entity is highly relevant to avoid malnutrition-related morbidity and mortality.
Pancreatic enzyme therapy for pancreatic exocrine insufficiency.
 

PMID: 17418056  April 2007

A mucosal inflammatory response similar to that elicited by gluten was produced by CM protein in about 50% of the patients with coeliac disease. Casein, in particular, seems to be involved in this reaction.
Mucosal reactivity to cow's milk protein in coeliac disease.
PMID: 17302893 March 2007
 
Conclusions Low faecal elastase is common in patients with coeliac disease and chronic diarrhoea, suggesting exocrine pancreatic insufficiency. In this group of patients, pancreatic enzyme supplementation may provide symptomatic benefit.
Is exocrine pancreatic insufficiency in adult coeliac disease a cause of persisting symptoms? PMID: 17269988 Feb 2007
 
Primary hyperparathyroidism may present with non-specific symptoms, and this may be one reason why patients with coeliac disease fail to improve despite compliance with a gluten-free diet.
Coeliac disease and primary hyperparathyroidism: an association?
PMID: 17148709 Dec 2006

"The major cause of failure to respond to a gluten-free diet is continuing ingestion of gluten, but other underlying diseases must be considered."

"If a patient is not responding well to a gluten-free diet, three considerations are necessary: (1) the initial diagnosis of celiac disease must be reassessed;(2) the patient should be sent to a dietician to check for errors in diet or compliance problems, because problems with the gluten-free diet are the most important cause for persisting symptoms; (3) other reasons for persisting symptoms (eg, pancreatic insufficiency, irritable bowel syndrome, bacterial overgrowth, lymphocytic colitis, collagenous colitis, ulcerative jejunitis, protein-losing enteropathy,T-cell lymphoma, fructose intolerance, cavitating lymphadenopathy, and tropical sprue) should be considered.Other causes for villous atrophy are Crohn's disease, collagenous sprue, and autoimmune enteropathy. "

"Of the 15 patients, 10 had small intestinal bacterial overgrowth, 2 showed lactose malabsorption causing the described symptoms, 1 had mistakenly taken an antibiotic containing gluten, and 1 patient each had Giardia lamblia and Ascaris lumbricoides."
Monitoring nonresponsive patients who have celiac disease. 
PMID: 16644460 April 2006 

DIAGNOSIS, DIFFERENTIAL DIAGNOSIS, AND THERAPY: It is essential to exclude alarm symptoms. IBS can be positively diagnosed with a sensitivity and specificity of > 90% by standardized questionnaires. Indications of PI-IBS are the acute onset of symptoms, fever, vomiting, diarrhea and/or positive stool culture. Differential diagnoses include lactose intolerance, small bowel bacterial overgrowth, bile acid malabsorption, celiac disease, giardiasis, chronic inflammatory bowel disease, collagenous colitis, and diverticulitis.
[Functional and inflammatory bowel disorders]
PMID: 16802539 Mar 2006
 

CONCLUSION: In patients with celiac disease partially responsive or unresponsive to GFD, SIBO and lactose intolerance should be suspected; appropriate investigations and treatment for these may result in complete recovery.
Partially responsive celiac disease resulting from small intestinal bacterial overgrowth and lactose intolerance. PMID: 15154971  May 2004  FULL TEXT

 
High prevalence of small intestinal bacterial overgrowth in celiac patients with persistence of gastrointestinal symptoms after gluten withdrawal.
PMID: 12738465  Apr 2003

 
"Of the 49 patients with celiac disease, 25 were identified as having gluten contamination. Additional diagnoses accounting for persistent symptoms included: pancreatic insufficiency, irritable bowel syndrome, bacterial overgrowth, lymphocytic colitis, collagenous colitis, ulcerative jejunitis, T-cell lymphoma, pancreatic cancer, fructose intolerance, protein losing enteropathy, cavitating lymphadenopathy syndrome, and tropical sprue. "
Etiology of nonresponsive celiac disease: results of a systematic approach. PMID: 12190170 Aug 2002

Giardia lamblia infection in patients with irritable bowel syndrome and dyspepsia: a prospective study. PMID: 16610003 Mar 2006

Giardiasis in patients with dyspeptic symptoms. PMID: 16425362  2005

Helicobacter pylori Infection in patients with celiac disease.
PMID: 16780559  Aug 2006

Duodenal intraepithelial lymphocytosis with normal villous architecture: common occurrence in H. pylori gastritis.
PMID: 15803187  Aug 2005

 The sensitivity of antibodies to casein, beta-lactoglobulin, and ovalbumin in active coeliac disease varied from 36% to 48% without significant difference between IgG and IgA antibodies.
Antibodies to dietary antigens in coeliac disease.
PMID: 3775259  Oct 1986