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An editorial by Peter Green and Joseph Murray appears in the July issue of Gastrointestinal Endoscopy.  The full text is available online:  "Routine duodenal biopsies to exclude celiac disease?"   This would be a good article to give to your GI doctor.

http://www2.us.elsevierhealth.com/scripts/om.dll/serve?action=searchDB&searchDBfor=art&artType=fullfree&id=amge03242&nav=full

I had the same experience described in this article.  When I was very sick one of the first tests I had was an endoscopy.   He took a biopsy in my stomach but not the duodenum even though it showed inflammation.  When I asked about this inflammation he said "That's nothing, we see it all the time".

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