we don't know, there are studies that have asked the exact same thing:
http://www.ncbi.nlm.nih.gov/pubmed/19924803
The study asks:
"Is mucosal pathology a secondary event?" or in English: "Are the clinical signs of inflammation seen during colonoscopy a consequence of deeper tissue inflammation?"
By the time someone is diagnosed with crohn's disease, there already tends to be transmural inflammation, so it's not ideal anymore to know. We know there is transmural inflammation in people with crohn's disease, because you can see it on MRI, some people have fistula, some people have had deep bleedings, and because people with crohn's disease are often in a lot of pain, pain that can't be explained by a bit of patchy inflamed follicles on the surface.
in early patients there is inflammation of peyer's patches, but that still doesn't answer if it's
inside out or
outside in
what about aphthae in people's mouth which often coincides with crohn's disease, are those
inside out or
outside in, we don't really know
it's a really important and good question, because if you could show that it's
inside out, you could prove that the intestinal flora isn't influencing the disease process, and you'd be able to argue that the bacterial antigen causing inflammation is in tissue