I've always looked to reasons such as dehydration from the recirculated air, early flight times, turbulence, and more recently, low blood sugar brought on my insufficient food onboard to explain the headaches and physical discomfort I've often experienced while flying. But, according to this Forbes article, I could just have mild altitude sickness.
That's because airplane cabins, particularly on long-haul flights, tend to be pressurized to 8,000 feet, an elevation at which, though most people don't experience anything like the nausea and vomiting associated with acute mountain sickness (which can occur at elevations above 6,500 feet), many people do feel physical discomfort caused by the body coping with less oxygen.
For reference, 8,000 feet is the elevation in Aspen, Colorado, and Machu Picchu, Peru. But in the air, you don't get the distraction of great skiing or wandering the ruins of an ancient city, only the kid in back of you kicking your seat.
Stress on the structure of the plane and increased aircraft weight are cited as two of the reasons cabins don't tend to be pressurized to lower elevations, but the article does mention that the newest Boeing aircraft is built to safely pressurize to 6,000 feet, which is apparently a far more comfortable elevation for the human body.
I'm all for anything that helps me arrive at my destination feeling good (or at least better), so I'll be following this story with interest, and will keep you posted.