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Some airlines won't let you fly up to 30 days before your due date. So if you are cleared to fly by your doctor in your third trimester make sure you have a note saying your doctor is allowing you to fly- some airlines require it!
My doc said no flying in the last month (?), but it depends on your pregnancy, i.e. if you're having twins they're more likely to be preemies. Some airlines have their own regulations so make sure you check that too...I'd check with your doctor and the airline before you make any reservations