The doctor can't always diagnose Crohn's from a colonoscopy alone, since in a colonoscopy they can only see your large intestine and sometimes part of the terminal ileum. There are other tests that can visualize your small intestine such as swallowing barium and watching by x-ray for it to pass through your small intestine, or the camera swallow test, where you swallow a camera the size of a pill and it transmits images throughout your entire GI system. Soemtimes they can also do a CT scan of your abdomen, and can visualize strictures, fistulas, and blockages that way. Go to the ccfa.org website (Crohn's foundation) and you can read about all of the diagnostic tests.
The doctor didn't see anything on my first colonoscopy, but was able to biopsy a part of my terminal ileum the following year and was able to confirm the blood results. Good luck, and don't stop asking questions!
50 yr. old female, diagnosed with Crohn's in small intestine and terminal ileum Sept-Oct. 2007. Also have IBS, and had Salmonella Dec. '07
currently taking Pentasa- 4 500mg pills per day, Metamucil and colace for constipation