Cervicogenic headaches are caused by referred pain — pain generated in the neck. It’s really a disease of the cervical spine. As pressure is placed on the neck during repetitive activities or a sudden trauma, damage may occur to the joints, muscles, ligaments and nerves. Typically, a cervicogenic headache originates in the top three vertebra of the neck. The nerves that affect the upper neck also supply the skin over the head, so the pain can affect the head, too.