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So, I was all set and ready for the surgery and then I got some bad news. The docs think now I might have Crohns.

I have done many tests in the past (colonscopies, flex sig, MRI, prometheus, endoscopies) - I was always told I had ulcerative colitis for the last few years. My inflammation includes the rectum, is continuous, no skip lesions, upper GI is normal, it is superficial inflammation and terminal ileum appeared normal. But in my latest colonscopy biopsy, it was found that, while my terminal ileum appeared normal, there is microscopic infammation in the terminal ileum and non-necrotizing granulomoutous inflammation in the terminal illeum and ascending colon. Only my rectum and sigmoid colon are visibly inflammed - the rest of the colon and terminal illeum are showing microscopic inflammation. And now the non-necrotizing granulotomous inflammation. Now, the doctor thinks I have Crohn's because of this latest biopsy finding. Not even indeterminite or Crohns colitis....but Crohns. Very devastated.

Has anyone had this type of finding? Has anyone done the Jpouch surgery with this kind of finding or similar finding? If so, how did it turn out? The surgeon said he will still do the surgery but my risks go up - but how much do my risks go up? I don't know. Does anyone know of statistics or anything on this that your surgeon may have told you?
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Cleveland Clinic still performs j-pouches on confirmed Crohn's patients depending on other risk factors. You can read more about their "j-pouch risk score" in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1360119/

My understanding is that one of the main requirements is that the patient have Crohn's colitis without small bowel involvement. I don't know much about microscopic inflammation and whether that would be considered a level of inflammation that would rule out a j-pouch.

If you don't have pancolitis and you're now being classified as Crohn's, perhaps a resection might be a better option for you? How severe is the disease in the rectum and does it affect the entire thing?

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