If there is one area that always comes in for a bashing when people run, it is the knee. Ironically the knee joint is actually rarely the problem and the fault often lies in the joints above and below the knee. Unfortunately the knee is between the ankle and the hip, two areas where people often lack the necessary stability (in and mobility to create good movements.
Over time imbalances start to develop as muscles begin to take on jobs that they are not intended to do, which can lead to inflammation and injury, and it sounds like this may be the problem in this case. When we run there is an increase in the amount of load that has to be absorbed by the body of up to 3 – 4 times our bodyweight. Combined with the large amounts of mileage that people often put in while training for a marathon and you have ideal conditions to reveal any poorly functioning muscles and movements. Rest and symptom reduction through ice and painkillers will help alleviate the pain, but they won’t make the problem go away. You will need to get an actual diagnosis on the injury from a physiotherapist who can perform an analysis of your running style and check out your muscle function, although it sounds like you might well have a problem with a little known muscle called the popliteus. The popliteus is a small muscle that is at the back of the knee joint and it is often the source of pain in runners. The good news is that this condition can be remedied by treatment from a physiotherapist, osteopath, or an active release therapist (find one at activerelease.com).
It also sounds like your hamstrings (the large muscles that run from the hip down the back of the thigh) are taking on more than their fair share of the work when you are running. This is actually quite a common problem as these muscles are somewhat prone to getting overworked. While the hamstrings should be helping out during running, they are not ideally placed to be doing all the work of extending the hips, which needs to be done by the muscles of the backside. Stretching of the hamstrings can help relieve this, but you should combine it with strengthening exercises for the buttocks. You must also ensure you warm up thoroughly when training.
Stretch the hamstrings by lying on the floor with one leg straight and the other pulled toward the chest. Slowly extend the foot towards the ceiling until you feel a stretch in the back of the leg. Ease into the stretch and hold for 2 – 3 seconds, repeating this ten times on each leg. To strengthen that backside, lay supine bending both knees to ninety degrees with the feet flat on the floor. Keeping the abdominals tight and the pelvis in a neutral position, squeeze the bottom and lift the hips off the floor. Hold for 2 seconds and then lower, repeating for 15 – 20 repetitions for up to 3 sets. Once you have mastered this you can progress onto exercises such as high step-ups to encourage the muscles to work as part of the whole body during movement.