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In one instance my company received an observation from a South American country because we had not removed the primary container from the secondary cartons. In response, we implemented a statement in protocols (if supported by data) that the secondary carton did not provide any stability protection and were then able to continue keeping material in the cartons for products supported in this way. That only applied that to zone IVb studies since that’s where the observation originated, and no other country had an issue.
Ultimately, for convenience I’d prefer to keep studies in the full packaging to avoid additional handling, but I have often seen the need to conserve chamber space since the cartons involved were very bulky for the small dosage contained within them. I’m talking 5 to 10 large bins of product vs. 1 or 2 bins if taken out of the secondary packaging. We’ve not had an issues from any inspector except that one IVb noted above. Still, a statement in the protocol justifying the removal from the secondary packaging can ensure you don’t get an observation if you do need to place them in the chamber outside of the full commercial configuration.