Knee's and thighs

Yes the knee's and thighs are being a big issue. I have not quit running for any length of time, I have new shoes and theres only been a bite of tread mill time. So what is it that makes it that it is very painfull untill about 3.75 miles. Because at 2 miles tried streching and got to sitting on my heals and didn't have the button because I could not get up. I had to go from sitting on the ground. This had better turn around an quick! It's been 3 weeks and getting worse.