Injuries from running

I understand running is a high impact sport. I have ran a full marathon and can easily run 10 to 15 Km any-day. But i genuinely have a doubt. Whenever i am running regularly, there is some part of my body paining. Be it knee, lower back or ankles.

Whenever i stop running for sometime, all the pain disappears. Am i doing something wrong here? Does everybody experience pain when they are running regularly?

The pain is all good if you are in to athletic profession. But me being a businessmen. Taking that pain to office is very uncomfortable throughout the day.

What are your thoughts on this? How do you guys avoid these common pain.