Sore knees from running are a very common problem not only in new aspiring runners, but even experienced well-seasoned athletes experience knee pains from time to time.
The best piece of advice that could be given for sore knees from running is prevention. If you get sore feet from running, the problem is probably in your footwear, always wear proper shoes designed specifically for running for proper shock-absorption. Take time to warm up and stretch your hamstrings, quadriceps and gluteal muscles before you run. Try to avoid downhill courses as they put unnecessary pressure on the knees.
If you continue to get sore knees from running, try switching your exercise regimen to include more swimming, low level cycling and exercises in a reclined position that do not put so much emphasis on your knees. If it seems like running and knee pain always go hand in hand, take a break from running altogether for 4-6 weeks and see if your condition improves. Consult a professional physical therapist for evaluation and treatment.
Sometimes, if you are a new runner you might get sore knees form running because your quadriceps and hamstrings are not strong enough. Try doing some exercises to strengthen these muscles. Self massaging the sore knees with anti-inflammatory ointment will increase blood circulation in the muscles and tissues to help them heal faster.
Sore knees from running could also be a symptom of it band syndrome or, in medical terms iliotibial band syndrome, an inflammation of the thigh tissue adjacent to the knee caused by repetitive movements and friction associated with running, cycling and other activities. If you suspect you get sore knees from running due to it band syndrome, consider running on a flat surface, pay special attention to warm-ups and stretches before and after exercising and strengthen your quadriceps and hamstring muscles.