An automated, ultra-low temperature freezer having multiple structural features that reduce heat transfer into the freezer, protect its internal mechanical devices against low temperature mechanical binding of their movements, allow defrosting and autoclaving as a result of only minimal changes to the conventional CO2 emergency backup system. A group of freezers are arranged so they can simultaneously provide an HVAC function. A vial management system allows biological samples or vials to be automatically placed in and recovered from the freezer and associates the temperature history with each sample or vial that it was subjected to during its storage.