I have sufered many knee ailments, so I feel your pain, literally. It sounds like it could be either patellar tendonitis or ITB, depending on where the pain is.
If the pain is directly below the knee, that is the patellar tendon and most likely the culprit. Just below the knee cap
(actually starting underneath it
) and running to the shin is the tendon in question. Press along it. If it is very tender, that is it. All I can say is ice the heck out of it, take NSAID's and ease off the running for a bit. If not taken care of, it can develop into a difficult situation and force you to stop. Causes for this can be various - increase in mileage to quickly, muscle imbalance, a specific trauma which was never given the chance to heal, etc.
If it is to the outside of the knee, but still below it, most likely ITB. This can be treated easily early on, but left untreated, it can also become a bear. You need to stretch and massage the heck out of it. Get a foam roll to massage it and stretch it numerous times through the day. Also, ice the knee and take NSAID's to reduce and inflamation
(you may not see any, but if it hurts, it is there
). This can be caused by muscle imbalance, over-pronating, sciatic issues, etc.
All that being said, it would still be a smart move to go see a doctor to have it properly diagnosed and nip it in the bud.
Good luck.