Please take your son to a pediatric GI. Our son had lots of digestive problems, and this was a critical step for us. In my non-medical opinion, it sounds like your son is having either GERD (reflux) or overall motility issues. How is his poop? Does he go every day? Does it look like hard little clumps or is it ever watery? Both are signs of constipation, which is very painful. You are smart to think about foods such as cow's milk triggering this. Our son couldn't tolerate either cow's milk or soy milk. We had to give him Pediasure and several meds. Pediasure costs a fortune (cheapest we found was Walmart) but many stores, including Walgreens, Safeway, and Target, have a store brand version for a bit less. Our doc had us give him Pediasure in lieu of either cow's or soy milk. It has tons of calories, too. There are other foods that could be causing issues, as could not chewing well enough or swallowing too much air while eating (because of talking a lot while eating or drinking while he still has food in his mouth). You son could also be having gas pains from swallowing air or from eating had to digest foods. The waking up at night and crunching his knees in pain sounds like constipation, gas, reflux, or all three. You might want to try keeping him on his back and moving his legs in a riding a bicycle motion to see if you can help him relieve some gas. We have had to do that for our 4.5 year-old recently because he had to have antibiotics (we're giving him yogurt with probiotics to help replace the good bacteria, too). As for lactose intolerance or IBS, both are unusual in kids this young bit not impossible. You can test for lactose intolerance but not IBS. I personally have both, and for all but the truly lactose intolerant (cannot have any dairy in any form w/out getting bad symptoms -- much more common in people of Asian descent than other ethnicities -- most of us are technically lactose maldigesters -- can have some without much problem but can't have high lactose content foods like straight milk or ricotta cheese), it is important that we get some dairy -- maybe a slice or two of cheddar or jack cheese. Also, yogurt w/ live cultures tends to have very little lactose (not sure it has any) because the cultures break down the lactose. Having a bit of dairy insures that the body continues to produce lactase, the enzyme that breaks down lactose. If you cut out all dairy, lactose intolerance can get worse. Again, a test (drink milk and then exhale into some monitor thing a couple of times over the course of a few hours -- it measures the levels of a gas produced, I believe, when your gut breaks down lactose) can give you an answer for that so that you do not limit dairy unnecessarily. Again, please try "bicycles" and seek help from a pediatric GI. With both my stomach problems and my son's, I have found that even the best general practitioners do not have the tools or knowledge to deal with slightly more complicated than average patients. I so feel you on this. It's so awful to see your child writhing in pain and not eating enough. If your son is falling off his personal growth curve for weight (regular pediatrician can tell you this if he/she has been tracking your son's growth appropriately), then your pediatrician should be able to get you in with a specialist more quickly. A pediatric GI can help you figure this out. Perhaps he/she will know what's going on right away or can go through an elimination diet process with you. Just so you know, the least allergenic foods are generally considered to be rice and lamb (though food allergies more commonly manifest themselves as rashes, congestion, or other typical allergy symptoms, not stomach pain) and the easiest to digest are bananas (not green!, rice, applesauce, and dry toast (known as the BRAT diet). Good luck!!!