Flattened villi but no coeliac??

Hi there
I have just had an endoscopy as I have suffered from stomach problems most of my teenage and adult life. Lately it's been incredibly bad heartburn with the sensation of food getting stuck on the oesophagus. It was confirmed that there was no abnormality upon investigation however, the gastroenterologist did say that the villi are flat and that she will be testing me for coeliac disease. I have been tested before for this and I don't have either gene for it. It's always come back negative. Could it be a gluten intolerance? So confused! I had Graves' disease (hyperthyroidism) which was treated about 11 years ago. I don't want to keep doing damage to my gut but not sure what else could cause this?? I'm a 38 year old female. Thanking you all in advance x

I've had both but negative. My doctor told me it is incredibly unlikely if I do not have either gene for it to have it.
Just wondering what the flat villi could mean?

I've had both the endoscopy biopsy and blood work as you stated!
They have come back clear, however I have the flattened
Villi. Again, just asking if anyone would know what else that could be caused from!!

Have been taking nexium on and off for a few years. I would rather find a cause to my gastro issues and not have to take medication that fixes one thing and causes another! Nexium side effects if you are one of the unfortunate ones to have them are horrendous.
My blood work has come back clear for coeliac.

Flattened villi can be seen in other conditions besides Celiac. Eosinophilic Gastroenteritis is one such condition. See www.APFED.org for more info.

Eosinophilic Esophagitis causes reflux-like symptoms and food getting stuck/choking. Eosinophilic Gastroenteritis can cause flattened villi and may or may not have other symptoms (nausea, abdominal pain, diarrhea, etc.).

It would be a good idea to discuss food allergies (milk, wheat, corn, soy, egg, tree nut, peanut, fish & shellfish are the most common) and environmental allergies (tree/grass/weed pollen, dust, animals, mold, etc.) with your doctor, as food & environmental allergies are known triggers for gastrointestinal or esophageal inflammation in those with Eosinophilic Gastrointestinal Diseases (EGID's).

Other conditions that can cause flattened villi include food allergy/sensitivity/intolerance, Immune Deficiency, gastrointestinal infection (giardia, TB, Whipple's, etc.), Tropical Sprue, HIV, Autoimmune Enteropathy, Radiation Enteritis, Crohn's Disease, Intestinal Lymphoma (which may be associated with Celiac), Zollinger–Ellison syndrome, etc. Basically, anything that can cause chronic inflammation in the gut can cause flattened villi.