I don't have a child (yet) but can tell you some very common food intolerances:
2) Dairy products
Of course, these are the most common intolerances - any food item could be the culprit.
Typical symptoms of food intolerances can include the following: nausea, diarrhea, vomiting, gas, bloating, constipation.....
Has you son been eating anything different over the last 2 weeks? Even a different brand of cereal, for instance?
In case he does have a food intolerance, you should consider keeping a diary of what/when/amount he eats (and drinks) and when symptoms set-in or get worse etc. This may help pinpoint the culprit - as well cutting out various things from his diet and seeing if that has any impact on symptoms.