I have a pain directly behind one knee after running - what could it be and what can i do? (i have the pain only after running.)

Knee pain post run: Several possibilities. One common problem is a baker's cyst causing pain in that area. Also tendinitis can cause this kind of pain along with several other problems. You need to see your doctor about this problem.

Meniscus tear w cyst: The fact that pain only occurs with running is significant. The considerable forces passing through the knee repetitively with each running step allow the weak spot in a potentially torn meniscus to form a juxtaposed cyst. The cyst can fill rapidly with joint fluid (akin to a bubble gum bubble) from the head of pressure in the knee. It should resolve with rest versus arthroscopic tear debridement.