As everybody else has said, position is important. Knee pain can come from having the saddle too low, so check that.
Another thing to consider, though, is what you're doing. It's pretty common for young guys to go hard all the time--if you're riding every day, and especially if you're pushing too high a gear, your knees are likely to complain.
Alternate easy rides with hard ones and take an occasional day off (you WILL NOT hurt your progress this way--your body needs time to recover from a hard effort). And watch your gear selection. Count the number of times your pedals go around (one complete revolution) in 10 seconds and multiply by six to get the revs per minute. More than likely, if you're a typical new rider, you'll get numbers like eight to 12 revs in 10 seconds, or 48-72rpm. Shift down (so you pedal faster but with less resistance) until you're in the 13-17 range for 10 sec, or 80-100rpm. That applies to all conditions--as your road speed increases, shift up to maintain the same cadence. When you climb, shift down but keep pedaling at the same speed.