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A headache was classed as a mild to severe pain in the head. Its causes were often vascular. (ENT: "Observer Effect") Medical advances made headaches uncommon or rare by the 24th century. (TNG: "The Battle")
In August of 2152, Ensign Travis Mayweather reported to Doctor Phlox that he had been having a little headache for the past couple of days. Though he merely wanted a simple analgesic to relieve it, Phlox, affected by the unusual radiation emanating from a trinary star system, insisted on running a series of elaborate scans on Mayweather and even performing a cerebral micro-section on his brain. The procedure, fortunately, was never performed, though Phlox's scans did provide T'Pol with insight as to how the radiation was affecting the crew of the Enterprise. (ENT: "Singularity")
In December of 2153, Corporal Amanda Cole reported to Doctor Phlox, complaining of a mild headache that she had been experiencing for about a week. Unable to find any other cause, Phlox suspected that the cause may have been Vulcan neuro-pressure inexpertly performed by Commander Charles Tucker III. (ENT: "Harbinger")
Captain Kirk complained of a headache during the encounter with the Klingons at Deep Space Station K-7. Upon arriving in sickbay, Dr. McCoy provided a pill, and asked whether the headache was due to Baris or the Klingons. (TOS: "The Trouble with Tribbles")
A hangover was a type of headache that was usually experienced after the person recovered from the consumption of too many alcoholic beverages, but could sometimes accompany the consumption or the inhalation of any type of mind-altering substance. Apparently the chief engineer of the USS Enterprise, Lieutenant Commander Montgomery Scott, was well aware, as a confirmed non-teetotaler, this well-known aftereffect of the consumption of too much alcohol. In 2269, after the Enterprise's ventilation system had been cleared of the remnants of Harry Mudd's love potion crystals and he got over his temporary infatuation with Lieutenant M'Ress, Scott complained of a "hangover to shame all previous hangovers". (TAS: "Mudd's Passion")
Early stages of the loss of her empathic sense due to the presence of the two-dimensional lifeforms were massive headaches, as experienced by Deanna Troi. Several other USS Enterprise-D crewmembers were also so afflicted. (TNG: "The Loss")
Benjamin Sisko suffered severe headaches in 2373 following exposure to a plasma burst from a holosuite console. The headaches were associated with odd synaptic potentials and post-neural shock syndrome, and also with a series of prophetic visions. Eventually, a neuropolaric induction was required to correct the condition. (DS9: "Rapture")
In Lieutenant Commander Tuvok's Insurrection Alpha holonovel, a holographic version of Commander Chakotay stated that the thought of spending seventy years on Voyager with Tuvok gave him a headache. (VOY: "Worst Case Scenario")