My 2 year old son has brown spots on his scalp his head is also flaky do you have any ideas of what if might be ?

Cradle Cap: Seborrheic dermatitis or "cradle cap" is the most probable cause with the symptoms you describe. You can use a Selsun Blue Shampoo three times a week for this. It contains selenium sulfide, which will help soften and remove the flakes. We could diagnose with more certainty with a photo through a Prime Visit!

Seborrhea capitus: Seborrhea capitus is a common condition in infants and young children, often characterized by dry flaking scales and plaques. This is generally managed by soaking the scalp in an oil for 5-10 minutes then gently combing with a fine toothed comb.