The endemic New Zealand kakapo is classified as ‘critically endangered’ and, in an effort to prevent extinction and restore the kakapo population, intensive handling of rare kakapo chicks is often utilised to reduce mortality and improve health outcomes among juveniles. Due to concerns that hand-reared chicks may not receive a full bacterial complement in their gut in the absence of regurgitated food from their mother, conservation workers feed a suspension of frozen adult faeces to captive chicks. However, the efficacy of this practice is unknown, with no information about the viability of these bacteria, or whether certain bacterial taxa are selected for or against as a consequence of freezing. In this study we experimentally determined the effects of freezing and reanimation on bacterial cell viability and diversity, using a faecal sample obtained from a healthy adult kakapo. Freezing reduced the number of viable bacterial cells (estimated by colony-forming units, CFU) by 99.86%, although addition of a cryoprotectant prior to freezing resulted in recovery of bacterial cells equivalent to that of non-frozen controls. Bacterial taxonomic diversity was reduced by freezing, irrespective of the presence of a cryoprotectant. While this study did not address the efficacy of faecal supplementation per se, the obtained data do suggest that faecal bacteriotherapy using frozen faeces (with a cryoprotectant) from healthy adult birds warrants further consideration as a conservation strategy for intensively managed species. Zoo Biol. 32:620–625, 2013. © 2013 Wiley Periodicals, Inc.