Soy in particular can be problematic for celiacs. I have heard it suggested that the long protein molecules are similar to gluten proteins, but I don't know if that is true or not.

Because of the damage that gluten causes to the gut in celiacs, undigested food molecules leak into the bloodstream that are not supposed to. Since they are not supposed to be in your bloodstream, your body sees them as invaders and produces histamines or antibodies to fight them. Which is (hypothesized to be) why a lot of celiacs have additional allergies or intolerances.

Although a coeliac soya beans are the one food that affect me even more and the last time I had soya milk I ended up in an ambulance as my throat was swelling shut.. I seem to be fine with other beans though which is good as I love my baked beans.

I take a probiotic in pill form, but some other options might be:

- coconut yogurt - the one commercial product I know of uses rice starch in it, but there are instructions to make your own online
- fermented foods like kimchi, sauerkraut, or homemade pickles

I don't know if you guys do this, but I always dump the first batch of water that I boil the beans in because it's got all the toxins that affect your system. You could try dumping the water and adding new and then see how you do with them. It's just a suggestion only because beans are tricky to cook.

Also, do not cook beans in a crock pot! They have to be boiled first. There's a really nasty chemical in them that can harm you and make you super sick. Let's just say, you'll need some major medications if you're eating them straight out of a crock pot without actually boiling them.

Once you boil them, you can pressure cook them or stick the whole pot in the oven for like 75 minutes at 250 degrees. They'll soften and will taste good. You can also continue to cook them on the stove. I would boil them for a good 10 or 15 minutes to get the chemical out of them. Dumping the liquid will also get rid of all the stuff that makes you really, really gassy. If after that, you still have troubles, you may want to try other beans to see if they affect you the same way. It may seem weird but sometimes you can have issues with one type and not another.

Oh, definitely wash the beans before you boil them. I read one bag that warned they could have wheat contamination. I think they were processed in the same factory as grains.

I don't know if you guys do this, but I always dump the first batch of water that I boil the beans in because it's got all the toxins that affect your system. You could try dumping the water and adding new and then see how you do with them. It's just a suggestion only because beans are tricky to cook.

Also, do not cook beans in a crock pot! They have to be boiled first. There's a really nasty chemical in them that can harm you and make you super sick. Let's just say, you'll need some major medications if you're eating them straight out of a crock pot without actually boiling them.

I am unable to eat gluten, but I eat beans all the time. So, it's not a gluten-thing. Moni may be right if you're not preparing them properly... that could affect you. I make beans all the time... and YES, I make them in my crock pot. To make dried beans, first, you must soak them a minimum of 5 hours, preferably overnight. Then, if you plan to make them in your crock pot, just boil them for 10 measley minutes first. That's all that's required to render them non-toxic. Not a biggie. If I couldn't leave my beans and soups going all day in the crock, I'd shoot myself. LOL

Here's the info from wikipedia, such as that is for a source, on the toxins to give you a short background:

The toxic compound phytohaemagglutinin, a lectin, is present in many common bean varieties, but is especially concentrated in red kidney beans. White kidney beans contain about a third as much toxin as the red variety; broad beans (Vicia faba) contain 5 to 10% as much as red kidney beans.[2]
Phytohaemagglutinin can be deactivated by boiling beans for ten minutes; the ten minutes at boiling point (100 °C (212 °F)) are sufficient to degrade the toxin, but not to cook the beans. For dry beans, the U.S. Food and Drug Administration (FDA) also recommends an initial soak of at least 5 hours in water, which should then be discarded.[2]
If the beans are cooked at a temperature below boiling (without a preliminary boil), as in a slow cooker, the toxic effect of haemagglutinin is increased: beans cooked at 80 °C (176 °F) are reported to be up five times as toxic as raw beans.[2] Outbreaks of poisoning have been associated with cooking kidney beans in slow cookers.[2]
The primary symptoms of phytohaemagglutinin poisoning are nausea, vomiting, and diarrhea. Onset is from one to three hours after consumption of improperly prepared beans, and symptoms typically resolve within a few hours.[2] Consumption of as few as four or five raw, soaked kidney beans can cause symptoms.[2]
Beans are high in purines, which are metabolized to uric acid. Uric acid is not a toxin as such, but may promote the development or exacerbation of gout. For this reason, persons with gout are often advised to limit their consumption of beans.[3] Uric acid is an important antioxidant in humans and, according to cohort studies, might be neuroprotective in cases of multiple sclerosis and Parkinson's disease[citation needed].

I'm a coeliac and cannot eat most beans, but I also have Crohns disease along with it, they cause painful bloating and other symptoms I won't go into!

I can tolerate small amounts of mashed or pureed beans which have been very well cooked, so something like home made hummus is ok in small quantities and I love mushy peas, but that's probably a British thing I guess!