If our validation is not written around the clauses of the standard, is this going to be non-conformity at our audit?

No. However, if the report does not cover all of the requirements of the standard (e.g. characterisation of the sterilisation equipment) the auditor will ask for this in addition. Reviews of sterilisation by notified bodies are based on the time needed – if there are non-conformities or missing information then the review costs can go up and the time taken to complete the review gets longer.

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