During the auditing process activities or documents will be identified which do not strictly adhere to the quality management system. These discrepancies should be recorded on the audit checklist with reference to the original documents. Objective evidence must be identified.

A discrepancy in the system is called a non-conformance. These may be divided further to include:

A major non-conformance - a serious breakdown in the system which will effect the quality of the test result. An example of a major non-conformance is a significant problem with the reception or identification of samples when they come into the laboratory.

A minor non-conformance - an issue which does not adhere to the documented procedures but will not critically effect the quality of the test result. This issue must be rectified but this does not need to occur immediately. An example of a minor non-conformance may be a staff members ‘skills register' which is not up to date.

During the audit the auditor may identify duplication in the system or ways in which the system can be improved. These issues should be documented on the checklist and can be discussed with the auditee as areas for possible improvement.