The most obvious change is the dramatic drop in air pressure as you take off.
A Boeing 737 flies at up to 41,000 feet, at is significantly higher than Mount Everest. At these heights, we would not be able to breathe.
Fortunately, thanks to Cabin Pressurization, the air in a plane is pressurized to a much more comfortable space 6000-8000 ft.
However, even this can be somewhat uncomfortable.
This is equivalent to moving instantly from San Francisco to Denver, or to hiking to the peak of Grand Teton in an hour.
On a physiological level, the reduction in air pressure causes the air in your body cavities to literally expand as you take off.
This is why your ear pops, why some people have belly pain, and why your cold symptoms get worse.
Effect of Reduced Oxygen in the Bloodstream
If you ever feel tired or have experienced muscle discomfort on a flight, a study shows that a minor lack of oxygen may be the culprit.
Because of the air pressure drop, you’re cells literally receive less oxygen from your blood. In a study published in the NEJM, patients who were monitored in a simulated flight environment experienced a nearly 5% drop in their blood oxygen.
When napping, the subjects' blood oxygen appeared to drop even further. The study found that that this, combined with changes in air pressure, was associated with fatigue and muscle discomfort.
Fortunately, your blood oxygen quickly recovers during landing, and the minor drop is completely harmless, albeit mildly uncomfortable, for the vast majority of passengers.
Long Flights and Blood Clots
One health issue that has attracted some publicity is the risk of blood clots during long flights. When you are sitting for up to 12 hours straight on a flight, your blood can spontaneously form clots, that can then travel to your lungs and get stuck.
Fortunately, most of these small clots are not harmful. However, on occasion, these can lead to more serious issues.
For patients who have known clotting issues or at high risk of clots, one possible prevention method are DVT stockings, which have been shown to significantly reduce the incidence of blood clots.