The following case study describes how a gene therapy manufacturer handled a possible Container Closure Integrity (CCI) issue due to deep cold storage at -80°C. The product was in clinical trial when the manufacturer discovered potential breaches in CCI. The identified issue occurred when a product vial from a stability study was punctured with a syringe and apparent overpressure in the vial moved the syringe plunger upwards. Referral to previous work involving a live viral vaccine stored at -80C lead to investigation of CCI . Scheduled clinical trial was halted and product batches were put under quarantine. Discussions with the national regulator were started and a root cause analysis was initiated with the objective to characterize the problem and propose corrective actions. The regulator would approve restart of the trial once suitable corrective actions were implemented.