We assessed the reliability and safety of subcutaneously inserted passive integrated transponders (PITs or microchips) for individually identifying Kakapo, Strigops habroptilus. The viability and location of the PITs inserted into 57 adult birds were assessed and the birds’ health evaluated after an average 16 months after implantation. Also, the growth rates of 21 chicks implanted at five weeks of age were monitored before and after implantation and their PITs assessed four months later. All transponders in both adults and juveniles were found to be working and located in the general area of implantation. No complications, health effects or growth rate changes were detected in either adult or juvenile birds. Kakapo are excellent candidates for this tagging system as their large body size allows the PIT to be deposited far from the insertion hole, and this combined with their flightlessness, possibly contributes to minimising transponder migration and loss. Although PITs have now been evaluated in several bird species, we suggest caution in generalising the results from this study to smaller, flighted species.