Headache pain can start in different structures in the head. The brain itself doesn't hurt, but other parts of the head do. Headache is a common symptom of illness, such as a cold or the flu. At other times, headaches happen without seeming to be connected to any illness. These are known as primary headaches. Examples of primary headaches include migraine and tension headaches. Very rarely are headaches a sign of a serious medical problem.
Referred pain has its source in one place, but is felt in another. For example, pain behind the eyes may actually be caused by tense muscles in the neck and shoulders. This means that the place that hurts may not be the part of the head that needs treatment.