Cryptic crossword clue
To begin with, it is an internal inflammation 9

The most common and most likely answer to this crossword clue is the 9 letter word ENTERITIS

I've seen this crossword clue in The Guardian
E
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R
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The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.
This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.

What does ENTERITIS mean?

ENTERITIS noun
  1. Inflammation of the intestines, generally the small intestine, that may lead to diarrhea.

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