I found out something interesting recently: that you can have IgE-mediated allergies to inhalants, even with negative skin and blood tests. This is called "local allergic rhinitis". The symptoms are similar to conventional allergies, and it's rather common: about 25% of people with rhinitis had local allergic rhinitis, in one study.
There's a continuing medical education course online about LAR. Local allergy has been dubbed "entopy" (as opposed to atopy). It probably can happen in organs besides the nose, see ''Entopy': Local Allergy Paradigm by DG Powe et al, 2010. The full text isn't available free online, but it's a good article.
The mucous membranes in the body are somewhat a separate compartment of the immune system, and different mucous membranes communicate among each other. Some vaccines are applied to a mucous membrane rather than being injected, for example sublingual and nasal spray vaccines for UTI's are being tested. Somehow the immunity is transferred from the mucous membrane in the mouth or nose to the mucous membrane in the bladder, and it works better than if the vaccine were injected.
Last I checked, it was uncertain whether local allergies are generated locally, or whether an excessive number of mast cells appear in inflamed tissue, and soak up the IgE in the blood.
The DG Powe article also mentions possible non-IgE mechanisms for local allergies.
Local allergies might be to blame for some delayed food allergies - the kind of thing where you try a food after going on a hypoallergenic elimination diet, and you start feeling bad maybe 1/2 hr to several hours after eating the food, and you stay sick for about 4 days. By "feeling bad" I mean a groggy, sick feeling where one can't think very well.
I have a theory about delayed food allergies: that they're local allergies in the GI tract, and the body tries to prevent the local allergy from becoming a systemic food allergy, because that could be life-threatening. So other kinds of antibodies, like IgA and IgG antibodies, come into play to try to prevent a systemic IgE allergy. After all, allergy shots raise the level of IgG antibodies, which reduce the IgE level in the blood.
So idea is that these IgG and IgA antibodies, while preventing a systemic food allergy, have vague symptoms like fatigue and difficulty concentrating. The body does something to prevent severe symptoms from these antibodies, so people often don't know they have a delayed food allergy. When someone does a hypoallergenic elimination diet, it changes whatever the body is doing to suppress the symptoms, and then when one tries the food again after the elimination diet, they get obviously sick.
The part about delayed food allergies being local allergies in the GI tract, is reasonable according to researchers. I don't know about the rest of the idea.
Local allergies might explain a lot of things, like some cases of chronic fatigue syndrome, "toxic mold" reactions, etc. Actually there are innate immune reactions to mold, as well as allergies, and these mold reactions may also promote allergies.
I've satisfied the diagnostic criteria for chronic fatigue syndrome, because of delayed food allergies. I probably have celiac disease - an autoimmune reaction to gluten grains.
I was sick for 4 years without knowing why, because of an inhalant hypersensitivity. Although I had allergy tests for years that were positive, in the past few years my allergy tests have been negative. My allergy symptoms have always been primarily mental and physical fatigue, not feeling fully awake. I have few specifically nasal symptoms, which made it hard to know what was going on.
When I came down sick 4 years ago, it felt a lot like allergies. It was a chronic bleary state, I felt all the time like I'd just been woken up at 2 am and I wasn't really awake. I went to a couple of allergists, and I was told I should be investigating non-allergy causes.
Eventually, by a long slow process, I found the cause. Part of it was mold that was getting into my food accidentally. But I was still sick even after I stopped eating the mold. Then I went to stay in a motel, and I found that after 5-6 days I got well! Then I went to the SPCA and cuddled dogs for 4 hours - and I got quite sick - the chronic bleary state was back again - and I stayed sick for days.
I've had dogs for 17 years. I had a mild dog allergy for years according to skin tests. Now I no longer have allergies at all according to skin/blood tests - but actually, I have a severe dog allergy. I got a lot more sensitive when I started to avoid dog dander.
I'm less sick from the dog allergy these days, with a lot of allergy medications and avoiding dog dander as well as I can while keeping my dog.
I could easily still be very sick, without a lot of persistent experimenting on my own. Sometimes doctors can't figure out health problems for you.
Local allergic rhinitis can be diagnosed by applying allergens inside the nose, but that may only be done in a research setting at present.