I'm just re-starting the program after finishing my first 5K (im working on increasing speed...because I was slow like a turtle, but I'm blaming that on the torrential rain) on sunday...when I first started, my knees hurt like hell...partially from my poor choice of running shoes and partially from my knees being angry at having to pull my big self around I guess. It gets better, or at least it did for me. Hang in there. You got this!