Can I ask what makes you think he is intolerant, just out of curiosity? I ask because one thing I have read a lot on and that I personally do believe (but know most others don't so do not want to debate, just sharing an option) is that children should not really be eating whole grains regularly as infants and toddlers. At about the age of 3yo they can start moving towards a diet of about 50% whole grains and the rest should not be. At about 5yo they can move towards a diet where all grains are wholegrain. The reasoning are that because their digestive systems are not able to handle that much fibre and it gives them gas, bloating, wind, and really messy poos. (Another reason is because wholegrains do tend to fill you up longer, and with LOs burning so much energy off and needing more fats in their diet, the white grains do get burned off and they eat again sooner and get more calories).
But the reality is that my DS has been slowly moving into some whole grains and more than one slice of wholegrain bread or one WG serving of something else and his digestive system is adapting. When he was an infant, if he got brown toast instead of white he had diarrhea within a couple of hours. Grainy bread, or seeded breads give him AWFUL problems. He has eaten rye bread most of the past couple of years and they are only about 50% whole grain and 50% regular flour and we still keep an eye on it all. When I bake I can only use half whole grain flour, he can only eat a bit of weetabix and so on. It is not that he is intolerant to it, just that his digestive system is taking a bit to get used to it. Whole grain bread for instance on average has about 2.3 grams of fibre per slice, and at 3yo kids need 8-13 grams of fibre. Two slices of toast, an apple, some whole grain pasta for lunch and they are there...
Anyway, not trying to "convince" and I certainly know there are LOs out there for whom this might not be true, but it might be something you want to read about and see if it gives you any answers.
HTH.
