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The Guidance document 'Claims Based on Non-Inferiority Trials' states that « In the event the non-inferiority study failed to demonstrate superiority in the primary endpoint, one should not use secondary endpoints to suggest superiority. » Does this still apply if the primary/secondary endpoints are unrelated (eg. primary endpoint is an efficacy measure, secondary endpoints are safety measures)?

Yes it still applies. Secondary endpoints should not be used from a failed study.

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