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By Mayo Clinic staffWhat causes primary cough headaches isn't known. Some researchers suspect that increased pressure in the head (intracranial pressure) during coughing or other types of straining may play a role.
Secondary cough headaches can almost always be traced to problems at the base of the skull, where the brain and spinal cord connect. Defects in the shape of the skull or the configuration of the cerebellum can result in a portion of the brain being forced through an opening at the base of the skull (foramen magnum), where only the spinal cord should go.
Some of these types of defects are called Chiari malformations. Many people who have Chiari malformations also experience secondary cough headaches.