This study describes the use of containment systems to prevent escape of microorganisms during lyophilization, thereby avoiding contamination of freeze-drying equipment. Cultures of Escherichia coli (JM 109) of an approximate cell concentration of 10 9 cfu/mL were suspended in 0.9% saline, aseptically dispensed into vials, double-wrapped in either medical-grade paper or Tyvek sterilization pouches and freeze-dried. An intentional collapse phenomenon was observed during the freeze-drying process, ejecting debris and aerosols from the vials, thus representing a worst-case challenge for containment. Following freeze drying, the layers of the pouches were tested for microbial contamination using 3 M Clean-Trace surface ATP analyzer swabs, surface swabs, and tryptone soya agar contact plates. The paper and Tyvek pouches were able to contain a maximum cell concentration of 1 x 10 6 cfu/mL of E. coli recovered from ejected debris. Some penetration through the first paper pouch layer was observed (although not Tyvek); however, this was successfully retained by the second, outer layer preventing contamination of the lyophilization apparatus and laboratory environment.