We use “gluten intolerance” when referring to the entire category of gluten issues: celiac disease, non-celiac gluten sensitivity and wheat allergy.

Celiac disease is an inherited autoimmune disorder that affects the digestive process
of the small intestine.

“Non-celiac gluten sensitivity” (what many call “gluten intolerance”) causes the body to mount a stress response (often GI symptoms) different from the immunological response that occurs in those who have celiac disease (which most often causes intestinal tissue damage).

As with most allergies, a wheat allergy causes the immune system to respond to a food protein because it considers it dangerous to the body when it actually isn’t. This immune response is often time-limited and does not cause lasting harm to body tissues.

Source : http://www.cureceliacdisease.org/archives/faq/what-is-the-difference-between-gluten-intolerance-gluten-sensitivity-and-wheat-allergy