Dissect the whole intestinal tract out of mouse very carefully.
It works best if you remove the small intestine from stomach and detach
the ileum just before cecum.  You can try and leave cecum intact with
upper large bowel, and carefully dissect the lower bowel away.

The small intestine should be rinsed with PBS, to remove all fecal matter,
which interferes with sectioning, tearing up morphology you wish to see.
If you have dissected the intestine without tearing holes in it, and it
is possible, 25 mls PBS on a syringe with a perfusion needle (rounded
tip, no sharp bevel, or dull and round off a large bore syringe needle)
is usually a sufficient rinse, we use 50  mls if we want to rinse IgA from
the lumen prior to IgA immunostaining.  If fecal matter is not removed
easily, just rinse from the opposite end, to push fecal matter to a wider
portion of intestine, it will rinse out quickly

I try to rinse from the stomach end towards cecum.  Cecum can be rinsed
along with the bowel, but I prefer to remove cecum, and insert a needle
into either opening or put a small slit in cecum to allow rinsing, you can
try to do this without damaging cecum, but it tends to ballon with PBS.
The bowel can be rinsed accordingly.

After the PBS rinse, fill the intestine with fixative, using a syringe
and dulled needle, drop fixative filled intestine into fixative.  We have
found this an excellent way to preserve the villi, and distend the intestine
a bit to get better midsaggital cutting.

I have done rinse/fixation with NBF or Carnoys (without chloroform)
also the Zinc Tris Buffer fixative for murine lymphocyte surface markers
(CD), no formalin used here!  The fixation, processing and sectioning
were much improved.

Gayle Callis