Could it be a food intolerance? My dc has runny poo on and off for years and I eventually moved him from cows milk to goats milk. It has made the world of difference. Maybe something to think about if he is otherwise perfectly well?
There are some allergy specialists who do skin tests, although I think not until 5/6years. Dairy allergies are very common, so you could just try switching to goat products for a few weeks and see.
A food diary would probably be useful to see if there are any obvious links between food/drinks and the runny poo, but that is a process of trial and error and cab be long winded. Best to have a conversation with your gp first I would think, just to be on the safe side.