You board at sea level, squeeze yourself into a seat designed with no respect for human anatomy, and a few hours later step out on another continent where your stomach thinks it’s lunchtime, your brain thinks it’s 3am, and your ankles have doubled in size.

Flying has become so routine that it is easy to forget how physiologically unnatural it is.

At cruising altitude, an aircraft may be travelling at around 35,000 feet. Inside the cabin, atmospheric pressure is lower, oxygen availability falls, gases expand, humidity plummets and movement becomes restricted. Fly far enough east or west and your
internal biological clock is left several time zones behind.

So, let’s take a look at the physiological journey your body takes as it flies through the
air.

TAKE-OFF: INTO THINNER AIR

As altitude increases, atmospheric pressure falls. The proportion of oxygen in the air remains constant. What changes is its partial pressure.

Commercial aircraft pressurise their cabins, but not to sea-level pressure. While cruising, cabin pressure is typically equivalent to standing at approximately 6,000–8,000 feet above sea level.

That means every breath still contains around 21% oxygen, but fewer gas molecules overall. The pressure driving oxygen from your lungs into your bloodstream is therefore lower.

In a healthy person, oxygen saturation might consequently fall from around 96–99% at sea level to roughly 90–95% during flight. For most people, this mild hypoxia causes no significant problem. The body compensates predominantly through subtle increases in ventilation and heart rate. But it may contribute to something almost every long-haul traveller recognises: fatigue.

Sitting still for ten hours, poor-quality sleep, noisy passengers, tannoy announcements, disrupted meal times and circadian disturbance all contribute, but the mildly hypoxic cabin environment can add to that general feeling of fatigue.

For people with significant heart or lung disease, severe anaemia or other conditions affecting oxygen delivery, the reduction can be considerably more important.

WHEN GASES EXPAND

Pressure changes affect more than oxygen.

As cabin pressure falls during ascent, gases trapped inside the body can expand by
approximately 25–30%.

You notice this most obviously in your ears.

Air inside the middle ear expands during ascent and needs to escape through the Eustachian tube. During descent, the reverse happens: external pressure increases and air needs to move back into the middle ear.

Swallowing, yawning and chewing help open the Eustachian tubes and equalise the pressure.

If you have a cold, sinus infection or severe nasal congestion, these narrow passages may be obstructed. Pressure cannot equalise properly, explaining why landing with blocked sinuses can range from mildly unpleasant to extraordinarily painful.

Your intestines obey exactly the same laws of physics.

Gas already present within the gastrointestinal tract expands as cabin pressure falls,
which can produce bloating, abdominal distension, cramping and increased passage of wind.

It isn’t always the aeroplane food.

YOUR GUT IN TRANSIT

The gastrointestinal system follows a circadian rhythm. Intestinal motility, gastric emptying, digestive secretions, appetite and glucose metabolism all vary across the 24-hour cycle.

Flying disrupts many of the signals that normally regulate them.

You may eat at unusual times, remain seated for hours, sleep badly, drink more alcohol or caffeine than usual and cross several time zones before breakfast.

Physical inactivity can also reduce the normal stimulus movement provides to bowel activity. Combine that with altered meal timing and circadian disruption, and constipation becomes a common travelling companion.

Hunger can become strange too. You can arrive somewhere at 8am with absolutely no interest in breakfast because, physiologically, your digestive system may still be several hours behind.

Your watch has changed time zones. Your intestines haven’t.

CABIN AIR AND DEHYDRATION

Aircraft cabins typically have a relative humidity of only around 10–20%, considerably lower than most indoor environments.

This explains the dry mouth, irritated eyes, cracked lips and nasal dryness that can appear several hours into a flight.

But there is an important distinction between feeling dry and actually being dehydrated.

Low cabin humidity is frequently blamed for dehydration, yet experimental evidence suggests the additional whole-body water loss caused by dry cabin air itself is relatively small.

So the cabin does not simply suck litres of water out of you.

The bigger issue is often behaviour. Long flights can mean drinking less water, deliberately restricting fluids to avoid repeated trips to the toilet, drinking alcohol or caffeine, sleeping for long periods or simply starting the journey inadequately hydrated.

Meanwhile, the dry air dries the mucous membranes of the mouth, nose and eyes, making dehydration feel more dramatic than the actual fluid loss caused by humidity alone.

Drink normally and regularly. There is little benefit in forcing litres of water purely because you are on an aircraft.

WHY YOUR ANKLES SWELL

Several hours into a long flight, you may discover that your socks have left impressive indentations around your ankles.

When you sit upright for prolonged periods, fluid moves into the legs while your calf muscles barely contract. Normally, walking causes these muscles to compress the deep veins, helping push venous blood back towards the heart — effectively acting as a muscle pump.

Sitting still removes much of that assistance.

The result is venous pooling and fluid moving from the circulation into surrounding tissues, producing the familiar swollen feet and ankles.

Usually, this is harmless.

But prolonged immobility also explains one of the more serious risks associated with long-distance travel.

THE REAL RISK OF SITTING STILL

A deep vein thrombosis (DVT) occurs when a blood clot develops within a deep vein, usually in the leg. If part of it breaks away and travels to the lungs, it can cause a pulmonary embolism (PE).

The major issue during long journeys is venous stasis: blood moving more slowly through the deep veins because the legs remain relatively immobile.

WHO research found that travel lasting more than four hours approximately doubles the risk of venous thromboembolism, although the absolute risk in healthy travellers remains small — around 1 event per 6,000 journeys lasting over four hours. Importantly, this risk is not unique to aeroplanes; prolonged immobility in cars, buses and trains also matters.

Risk increases when additional factors are present, including previous DVT or PE, recent surgery, active cancer, pregnancy, oestrogen-containing medication, obesity and inherited thrombophilias.

This is why movement matters.

Walking periodically, flexing and extending the ankles and repeatedly contracting the calf muscles aren’t meaningless pieces of in-flight advice. They mechanically help venous blood return towards the heart.

WHY YOU FEEL SO EXHAUSTED AFTER DOING ABSOLUTELY NOTHING

One of the stranger things about long-haul flying is emerging exhausted after spending most of the previous twelve hours sitting down.

But physical inactivity is not the same as physiological rest.

During a flight, you are exposed to mild hypoxia, constant background noise, vibration, restricted movement, an unfamiliar sleeping position, interruptions, altered meals and often fragmented sleep.

And if you have crossed several time zones, there is another problem waiting when you land.

SLEEPING AT 35,000 FEET

For nervous fliers – or anyone hoping to sleep through a long-haul flight – sedatives can be tempting.

Prescription drugs such as benzodiazepines can reduce anxiety and cause sedation, while sleeping tablets such as zolpidem may make it easier to fall asleep. But sedation is not necessarily the same as normal, restorative sleep, and these medications come with drawbacks in an aircraft environment.

Sedatives can impair coordination, reaction time and judgement, cause residual drowsiness after landing and occasionally produce paradoxical agitation rather than calm. Combining them with alcohol increases their sedative effects. Prolonged sedation can also mean less movement, which can be dangerous in people already at increased risk of DVT.

For fear of flying specifically, medication may suppress anxiety during the flight without treating the underlying phobia. Psychological approaches, particularly graded exposure and cognitive behavioural therapy (CBT), instead aim to change the fear response itself.

For some people, medication may have a role, but sedating yourself through a flight is not as straightforward as simply sleeping through it.

JET LAG: YOUR BRAIN IS STILL AT HOME

Deep within the hypothalamus sits the suprachiasmatic nucleus (SCN) – the brain’s master circadian clock. It helps coordinate approximately 24-hour rhythms throughout the body, influencing sleep and wakefulness, melatonin secretion, cortisol, body temperature, appetite, digestion and cognitive performance.

Its most powerful environmental signal is light.

Light detected by specialised retinal cells travels along the retinohypothalamic tract to the SCN, providing information about environmental day and night. The SCN then helps synchronise clocks throughout the rest of the body.

Normally, your internal and external time broadly agree.

Cross six time zones in ten hours and they suddenly don’t.

At 11pm in your destination, your circadian system might still believe it is 5pm.

Melatonin secretion, body temperature, alertness and digestive activity are therefore
occurring according to the wrong schedule.

That mismatch produces the characteristic combination of insomnia at night, sleepiness during the day, poor concentration, reduced performance, altered appetite, gastrointestinal disturbance and fatigue.

Different organs may also adjust at slightly different rates, meaning jet lag is better understood as a temporary desynchronisation of multiple biological rhythms, rather than simply being sleepy at the wrong time.

EAST VS WEST

Your circadian clock isn’t exactly 24 hours long. In most humans, its intrinsic period runs slightly longer than 24 hours, meaning the body generally finds it easier to shift bedtime later than earlier.

Flying west usually requires a phase delay. If you fly from London to New York, local bedtime arrives later according to your original body clock. You need to stay awake longer.

Flying east requires a phase advance. London to Singapore asks your brain to become sleepy substantially earlier than it expects.

That tends to be harder.

This is also why appropriately timed light exposure is one of the most powerful ways of shifting the body clock. Depending on when it occurs relative to your biological clock, bright light can push the circadian rhythm earlier or later.

Melatonin works on the same clock from the opposite direction: it acts as a biological signal of darkness. Timing matters enormously, which is why simply taking melatonin because “it’s bedtime here” is not always physiologically sensible.

LANDING DOESN’T MEAN YOUR BODY HAS ARRIVED

As the aircraft descends, cabin pressure rises again. Oxygen availability returns towards sea-level values. Expanded gases contract. Your ears equalise. You stand up, your calf muscles get back to work and the temporary physiological effects of the cabin environment begin to disappear.

The only thing left behind? Your body clock.

Flying is an extraordinary demonstration of how adaptable human physiology is. Within hours, we can move through reduced atmospheric pressure, mild hypoxia, extreme dryness, prolonged immobility and an abrupt displacement of environmental time – usually with little more than swollen ankles, a bloated stomach and an overwhelming desire to sleep at lunchtime.

The aircraft may cross the world in a day. The body takes a little longer to catch up.

Information and other content provided in these blogs should not be construed as medical advice and should not be considered a substitute for professional medical expertise. If you have any medical concerns, you should consult with your health care provider.