The most common anatomical cause in a child under two is metatarsus adductus, in which the bones of the middle part of the foot deviate inward. If the in-toeing doesn't diminish or becomes severe, stretching, corrective shoes, or, rarely, casting may be recommended. As with metatarsus adductus, this problem usually resolves itself as your child's leg muscles get stronger with age. If it doesn't clear up after approximately nine months of walking, or if the inward rotation is severe enough, his pediatrician may need to evaluate him again. By the time he's three or four, he may no longer have the problem.
Parents usually notice in-toeing by the time their child is three years old.
Except for severe cases, a child should walk without any problems by the time he's seven or eight. If not, stretching and strengthening of the leg muscles usually improve the situation. Rarely, a child will need bracing or further intervention. I suggest you bring it up again. Your son may have had one of the aforementioned conditions, which was normal at the time, and your pediatrician may have been waiting for the in-toeing to cure itself.