Jennifer, it was actually a suggestion by the l/c at my ped's office. I was totally against the suggestion at first, but she convinced me that more than 60% of milk protein intolerant kids are soy protein intolerant too. When I tried it, he changed almost overnight. Soy is hard to cut out because it is in so many processed foods - and healthy foods. The next thing I realized is how much better I feel, and wonder if maybe it wasn't me with the soy intolerance too? Max does fine with cows milk now, but I haven't soy trialed him.
The other possible culprits are wheat, egg, fish, nuts, citrus (although sometimes only uncooked, tomatoes included).
Some of the more genetically engineered crops - soy, corn - are showing up with higher allergies now.