Skull indentations can be caused by injury, surgery, congenital birth defects or trauma during childbirth, according to Healthline, John Hopkins Medicine and the National Center for Biotechnology Information
It is not uncommon for babies to have unnoticeably small indentations in their heads as they are growing. These are known as fontanelles or soft spots, and they close up as the baby's head grows over the first two years of life. If the fontanelles are visibly indented, this is an urgent medical problem known as sunken fontanelles. It can be caused by dehydration or malnutrition, according to Healthline.
The most common cause of congenital indentations is trauma in the womb or during childbirth, according to the National Center for Biotechnology Information. Skull indentations can be repaired through a procedure called cranioplasty, according to John Hopkins Medicine.