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The sphenoid sinus (yellow) is the deepest sinus, sitting at the very back. When it gets infected, it can cause headaches at the back of the head. Its drainage runs almost straight down the throat, so people with a sphenoid problem often have a long-lasting cough and headaches in the back of the head. The pituitary gland — a small but important hormone gland — sits right on top of this sinus.