Not sure if they care about blood clots that are still in your legs, but there is another good thread about ones which get dislodged. My advice is keep your legs moving on longer flights (stand up, or walk around if you can- take a trip back to the lav for aircraft equipped with it), read somewhere that sitting for 2-3 hours can put you at risk for clotting and DVT, keep hydrated too. This is why all of the airlines serve water on the long haul flights, in fact the inflight magazines generally have an article about it in the back. Another advantage to staying hydrated (about 2 L of water a day) is that it will prevent kidney stones. Seeing your primary doctor first would be a good idea, they may have more insight into it...plus it is better than telling the AME/FAA that you might have a potential issue.

http://www.airlinepilotforums.com/pi...at-pilots.html