Yes, sleeping position affects a baby's head. If you let your baby change positions frequently, you can prevent the flat head syndrome. Additionally, you should consider any other factors that may cause the flat head syndrome, including birth defects and genetic abnormalities. AAP recommends that infants sleep on their backs to prevent Sudden Infant Death Syndrome (SIDS). It's safest for babies to sleep on their backs because it opens the airways and reduces the risk of choking.