My 14 year old daughter has been diagnosed with eosinophilic esophagitis. It is an allergic type reaction that causes increased white blood cells, which can occur throughout the digestive tract. It is a rare disease (1 in 10,000) that is increasingly being diagnosed in children. It can result in difficulties swallowing, abdominal pain, vomiting and diarrhea. Diagnosis is not always clear cut but it is done through multiple biopsies, where they then count the number of eosinophils per high power field. It is best done by an doctor who has experience with the eosinophilic gastric diseases, because it is easy to miss it.
For more information, see the following websites. Cincinnati Children's (Dr. Putnam) and CHOP (Children's Hospital of Philadelphia) are the leading hospitals for treatment.
www.curedfoundation.org/
http://www.apfed.org/news.htm
Has your son been tested for celiac disease? My daughter was also diagnosed with celiac disease, this summer. This disease can also be hard to diagnose. Diagnosis is done through a celiac panel of blood tests, that is usually followed up with an endoscopy and biopsies, looking for villi damage. It is important that gluten continues to be eaten until after the blood test and biopsy, otherwise the test may be negative due to the diet.
Good luck figuring this out. My daughter has had severe stomach pain since late last winter. Even with treatment for the EE and celiac disease, she is still in pain. We are seeing a new GI doctor this week, so hopefully we will get some good advice and a something that will actually help her.