Our bodies change, and so does our flexibility. Bike fit is usually one of those things that we sample with and more often than not we get it wrong. We wonder why our knees, neck and lower backs hurt as well as our feet, the OUCH is often associated with a poor fitting bicycle. Two years ago I decided to take me and my trusty steed up to Contender Bikes in SLC for a Pro Fit, I knew they where working with Dr. Max Testa and thought I'd give it a go. I was amazed with the high tech video and sticky things all over my body in order to measure me on the bicycle. After the fitting they allow you to keep the DVD as well as a print out of the measurements so that you can set up another bike if need be. The cost at that time was $125.00 - After spending the money you would think I'd have been upset to find that the only thing wrong was that I was running my saddle a bit low. I wasn't upset at all and after all these years was happy that I had been doing some things right with my fitting and it really was money well spent. If you're serious about injury free miles and getting the most performance out of your trusty steed then I highly suggest that you get a professional fitting. So often we spend the BIG money on a nice bike, helmet and shoes and NOT on the most important thing of all, the fit.
When you purchase a bike it is usually set up for a general classification of body type and usually people are not "off the rack" sized. It's cheap to change the stem, bars and saddle and usually these are the culprits. Don't forget a cleat fitting is a MUST because many a knee injury is associated with improper fitting cleats and shoes. If you've never had a pro fit, it might be a good consideration to start the season out looking like you and your bike are made for each other.
PS- That quick fit they gave you when you purchased your bike is NOT a pro fit, consider that a free saddle adjustment that more often than not is incorrect.