Kiwi, thank you for this. I appreciated it. I found it a few nights ago, and asked a friend to get me the article. As soon as he gets it to me, I'll read it. It is the only thing I've read that concerned me, even though it's n=1, though it's more like n=1 x4, since there were three other post FMT adverse outcomes. It is a reason to pause at least. I read about it here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365524/ and then read the original study. This is the relevant bit:

"G&H Are there any potential risks of fecal transplantation that clinicians need to keep in mind?"

"LJB Fecal transplantation is normally performed via colonoscopy, so the risks associated with colonoscopy will also apply to fecal transplantation, but these risks are minor and well known to endoscopists. Otherwise, there have been no significant adverse side effects definitely attributable to fecal transplantation. In the study we presented at the 2011 ACG meeting, we found that 4 of the 77 patients in our study developed some kind of immune disease following their fecal transplantation procedure. There was 1 case of peripheral neuropathy, 1 case of Sjögren syndrome, 1 case of rheumatoid arthritis, and 1 case of idiopathic thrombocytopenic purpura. While these adverse events bear consideration, I do not know if they were definitely attributable to fecal transplantation."

I'm not sure what to think. I think that the microbion affect immunity, so much of our immunity is/originates there, so though I get the caution of the physician, I think they need to realize this essential truth. But, again, I get his caution, as there's no evidence that the FMT caused the immune issues and these were all pretty sick people and the immune issues could have easily arisen from the initial infection and/or adverse impact on their microbiom, or even earlier and remained dormant.

But you're definitely right that it's worth considering, perhaps more seriously than the studies authors have done.

Edit/Addition: It seems all there is is the poster. I just read it, but want the published final paper, though I may have to contact the author. It seems like the PN resolved itself 6 months later and that the patient was already quite ill at the time, not just with CD. But still a note of caution, especially since there were three other autoimmune issues post FMT.