Hi M.,
What a great question! One I have grappled with and have some information for you.
My instincts and research led me to IgA STOOL testing for food problems as a practical fundamental root cause approach to the problem. From the day we are born, most of us are putting foods into our mouths (or having them put in for us) that cause autoimmune responses in the body. This aggravates the immune system for a lifetime and can cause other downstream allergy reactions, whether it be to pets or to a piece of asparagus, as well as systemic illness from ear infections to autoimmune diseases like asthma.
As a first step, there are only a few major underlying problem foods that need to be tested (gluten, casein, soy, eggs, corn, yeast etc). The best test for this is not blood or skin scratch. It is an IgA STOOL test. The only lab I know of that does this is actually local in Plano - Enterolab. www.enterolab.com. The doctor who started the lab used to be head of GI research at Baylor. He began to see in his research and pracice that conventional methods of testing (blood, skin, endoscopy) were "missing the boat" on most people. He theorized that if your gut is reacting to something poorly, you need to test where the reaction is occurring - IN THE GUT. Since 80-90% of your immune system is located in the gut, this makes LOTS of sense. So, he created a practical stool test you can do at home. His research is proving up his theory - regular GI and allergy doctors are missing the boat regarding diagnosis and treatment recommendations in this area.
The test is easy. No doctor referral needed. Everything is done by mail and email. It is especially great for kids, since it is not invasive like the other testing methods. Insurance may or may not cover it.
You can do a rotation elimination diet, but this is difficult for most people to implement. There is also a mental attitude adjustment to changing lifestyle patterns such as eating. It is easier to do when you see a test result in black and white. Besides, many reactions are delayed and difficult to connect. But it is cheaper than lab testing!
Most people who truly understand food problems think very little of skin scratch testing. They say "if you want to know what your skin is reacting to, do a skin scratch test." It is not an appropriate method for testing for foods. That doesn't stop the fleet of allergy and immunology doctors from pushing them, along with attendant unreliable blood tests. But what else are they to do? Go back to med school and choose a different specialty? There is no financial incentive for them to admit the patient has a gut problem, where most of the immune system is located. They wouldn't have any work left - they would have to refer everyone over to the GI doctors. Not very good for their bottom lines. I rarely hear of a person achieving full health with a skin scratch doctor. At best they report "some improvement" and the "problem is at bay." That's not real health. It is coping.
There is also IgE or IgG allergy testing. It is my understanding that these only test for 'histamine" type reactions. These are food sensitivities that result immediately within minutes or 1-2 hours, and are usually short term. They are also alleviated with an anti-histamine. They also usually test for some crazy number of things - 40 or 50. Very often they report back to a person that they have to avoid an inordinate number of things, which is often very difficult. Histamines are not released with IgA reactions, which leads to latent, or "hidden" food intolerance problems.
I personally don't believe eliminating 30 things from your diet and life is practical or necessary, and creates a consufed frenzy of response in patients everywhere. Most people have trouble complying, get frustrated, and resolve themselves to living a life where feeling good and healthy is sacrificed. It's better to focus on the hidden underlying food problems. The biggest of these are casein (dairy) and gluten, with half the US population having a problem with these alone. If you eliminate these, the body recovers and other problems go away. Then you can evaulate if there really are other things that cause histamine reactions, and consider pursuing those. If you've got someone with systemic health problems, IgA testing for underlying "hidden" food intolerances is the better way to go.
Good luck.