There are a number of issues relating to you and your body during the flight itself. This link details these for example changes within the pressure of the ear canal during flight.
http://www.britishairways.com/travel/healthdur/public/en_gb

Jet lag

Many travellers do not experience any aspects of Jet Lag, the shorter flights do not expose the traveller. However, the effects are real and can be disturbing and disruptive to the first stages of your travel.
http://www.medic8.com/healthguide/articles/jetlag.html

DVT – deep vein thrombosis

If blood clots inside the veins, usually of the lower legs, then this is what is called a Deep Vein Thrombosis.
http://www.traveldoctor.co.uk/flights.htm

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