Some negative side affects for your health when flying are:
# DVT (Deep Vein Thrombosis)
One of the most frightening side affects of all is DVT which is a blood clot blocking blood flow in your legs which causes swelling. The results are damaged lungs and other organs. The longer and the more often you fly, the higher the risks.
# Ear Pain
Due to changing cabin pressure especially during takeoff and landing, pressure will be build up in your ear canal which causes pain if it cannot be released.
Since the humidity inside aiplanes is lower then at any other place you are usually going, you are likely to suffer from dehydration very quickly which will be visible through a dry (and bleeding) nose, dry and red eyes and a dry mouth. The results here are headaches, low blood pressure and fever. You are also more susceptible to infections.