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The standard cuff is a centimeter or two, not a few inches (that is the cuff length that leads to very serious issues).
It is interesting that you mention this because my GI doctor, after my most recent scope in June 2014, complimented the work of my surgeon in leaving a very short amount of cuff. My GI doctor trained at Cleveland Clinic and Dr. Shen is his mentor, so he has seen many, many J pouches and does not shoot from the hip with such opinions.
I have never had Cuffitis, to my knowledge, despite consuming vast amounts of antibiotics over the last 20 years. I have essentially been on antibiotics nonstop since 1995. They did see some inflammation in the Cuff in June 2014, and biopsied it, but they came back negative.
My GI told me if a cancer ever develops, the retained rectal cuff is where it will develop- because I had dysplasia in my colon, I am in the risk category. The Cleveland Clinic did some study on this and they did find some cancers developed in the rectal cuff of J Pouch patients. However he told me it was mostly people that had severe pouchitis for many years.