Cryptic crossword clue
Little hesitation probing doctor attached to unpleasant religious institution 9

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

I've seen this crossword clue in Independent
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Buddy explains!

The straight part
We know that "religious institution" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case religious institution = monastery.
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 MONASTERY mean?

MONASTERY noun
  1. Building for housing monks or others who have taken religious vows

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