Is the pain specific to your cycling? Does it go away when you get off the bike? If not, then you should seek professional advice.
Generally, there are two basic reasons for cycling-specific knee problems...
1. The bike isn't adjusted properly. Is your saddle too high, or too low? Even minor changes can make a big difference. Are your cleats in the right position? If not, they could force your knees into an unnatural angle. Some pedal/cleat systems offer more lateral float than others, allowing your legs to find a comfortable position.
2. The cyclist is pushing too big a gear. Would this apply to you? Mashing high gears at low RPM's can cause problems. Have you tried spinning lower gears at higher RPM's?