Why do my knees ache every time i start running or walk down the stairs?

Knee pain: There are many causes of knee pain -- what you are describing sounds like arthritic pain (depends on your age) and is best evaluated by your primary care doctor. Exam +/- imaging will be helpful in diagnosis.

Chodromalacia: When you up and the steps a lot of stress applied to the joint between the knee cap and femur, so any problem in that joint show on those motion because they go are stress and also in squatting.

Knee Pain: If you are younger, some cartilage damage, with motion under stress such as running and stairs, or tendonitis is more likely. As you get older, and the more you have used your knees for athletic pursuits, the cartilage can wear thin, and the bone can rub on bone, osteoarthritis. Orthopedist, with x-rays, mri, and a arthroscope can let you know, what the damage is, and how to improve the problem.