I say, no, don't reintroduce gluten for the test. He can have blood drawn to determine if he is celiac, or genetically inclined to be. By having the test, if he is diagnosed as celiac, not only will he be pegged with a pre-existing condition, that could make his healthcare skyrocket for the rest f his life, the only treatment for celiac is to not consume gluten. Dairy intolerance and gluten intolerance often go hand-in-hand. Eventually, years later on a gluten-free and dairy-free diet, he may be able to tolerate cheese again, as his intestinal tract heals. Most of my family is celiac and can't handle cow dairy, but can handle goat's milk and goat cheese. Since he's had negative celiac tests before, but going grain-free makes him feel better, he should stay grain, dairy and sugar free. I would, however, encourage further medical investigation to find out if he has other autoimmune disorders or gastrointestinal damage/infection.

Does your son know he is allowed to fire his doctor? He's a minor, and doctor-patient is a power relationship many an adult has trouble negotiating. Maybe he needs you to tell him that it would be ok to seek a different opinion, try a different experiment, go to the nearest med school library and check out a few armfuls of books... To take charge instead of letting some idiot with a pedigree dictate his life choices.

As a child, my pediatrician told my mom to give me Ensure or Boost all the time. I suffered constant fatigue, joint pain, etc. until going completely gluten, grain, and dairy free. Dr. Smith (his real name) never even bothered testing me for food intolerances or celiac. I'm afraid you really have to be your own healer, researcher, and advocate. (But thank God your son has a good mom too!)

I think you have your answer about gluten and dairy already from your son's repeated experiments. He knows how his body reacts to this stuff. He needs to know he is allowed to listen to it. First, the two main blood screening tests for celiac have an 8% false negative rate (they're good but not perfect). Second, there is no good reason to make yourself sick going for the diagnosis if you already know what makes you sick. It is malpractice to tell a patient to make himself sick. The first rule of medicine is to do no harm.

I also take a number of supplements. Reading James A. Duke's books (eg, Green Pharmacy and Herbal Handbook) was really helpful in identifying what foods/supplements to experiment with next, to trouble-shoot problem by problem.

There are tons of ways to add calories other than eating grains. There are tons of tests to run other than celiac if you've already checked that, and tons of lifestyle experiments to run to see what makes you feel better rather than doing something you know will make you feel worse. But first, just my two cents, your son needs a new doctor.

Good luck.

Edit: Another thing you might try if you haven't already. Go through your bathroom as well as your kitchen. Read every last shampoo bottle and pill container ingredients list. Gluten in particular and grain matter in general is in so much stuff, it's unreal. Whether your son is gluten intolerant or celiac - and it sounds like he has the expertise about his own health to know that he is one of the two - he needs to avoid exposure to gluten in all its many forms. I have negative celiac bloodwork, and I literally get visible bloating, GI upset, and hives from using Aveeno lotion. With oats. That I used for years. Find the poison and throw it away!

Not uncommon at all for celiacs to be underweight and or underdeveloped due to being so sick from the digestive issues and upset caused by the gluten allergy. Like Lyndsay said, other allergies are often co-occurring. In addition to blood testing, has he had any sort of formal allergy testing by an immunologist/allergy doctor? I'm not sure this current doctor knows enough about celiac from the sounds of it if they want him to "eat wheat" to get a better result. Even if he isn't eating it regularly, he may still have the remnants of past bouts of the disease lingering that he is currently fighting off. Best thing you can do now for him to help him grow is avoid processed garbage like Boost and encourage the foods he does like Paleo-wise. Make those for him and encourage him to expand his palate as he is ready. He's a teen so he'll be fickle, but hopefully grow into it. :) And good luck. I bet this is frustrating as a parent!

1. Stay off all gluten and all grains. He might not be celiac, but have gluten sensitivity. Gluten can do more damage than just his gut.

2. I would go with GAPs (strict GAPS for now).

3. I would supplement his diet with fermented cod liver oil and butter oil to see if it helps him to grow.

4. I would include active probiotics/some fermented foods. Make sure the bacteria in probiotics is still alive.

5. Bone broth three times per day will help him with gut healing and other issues.

The blood tests for celiac disease will yield a negative if your son has been eating gluten-free. The only test that would be valid is the genetic test and it is only a risk predictor, not definitive. The usual guideline is to eat gluten daily for 4 to 6 weeks before blood testing. Even then the tests have ridiculously high false negative rates especially with patients having only partial damage to the small intestine. An official diagnosis can be helpful in certain cases: if you itemize on your US taxes the cost difference for GF food can also be deducted (but with paleo this hardly matters), dorm living could require proof for needing the diet - you might get a discount if they can't provide proper meals, other institutional settings like hospitals or nursing homes, some patients psychologically need the DX to stay on diet. Otherwise, you don't need the tests to actually eat gluten-free of course.

You might also wish to look into non-celiac gluten sensitivity:

http://www.ncbi.nlm.nih.gov/pubmed/22825366

http://forums.glutenfree.com/topic217.html

http://www.celiac.com/articles/23033/1/Non-Celiac-Wheat-Sensitivity-It-Exists/Page1.html

GAPs sounds like a good place to start if you can get enough calories into him with it. I'm not that familiar with it. I like SCD but it does include dairy though only fermented dairy. I only do a bit of yogurt.

You might wish to peek at these blogs too: http://comfybelly.com/2010/11/cut-out-cookies-using-almond-flour/#.UEdWHlSBWXV

http://milkforthemorningcake.blogspot.com/

Good luck!