Translocation of the koala (Phascolarctos cinereus) has been a controversial measure that has been utilised for over a century in the southern states of Australia. Recently, translocation has been suggested as an option in the management of some declining northern koala populations. Infectious diseases present within donor and recipient populations are important factors that must be considered when planning any wildlife translocation. In the koala, infectious diseases, caused by the bacterial pathogen Chlamydia pecorum, are one of the key threats to koala conservation. In recent years, significant progress has been made in understanding the biology and epidemiology of koala C. pecorum infections revealing complex patterns of infection and disease and the potential for ‘spill-over’ from C. pecorum infected livestock. Here, in light of this new epidemiological data, we provide a discussion of risk assessment and management in the context of enzootic chlamydial infections. We conclude that without careful investigation and management, significant risk of pathogen transfer is likely, especially for larger and more distant translocations. Thus, for such a programme to be appropriate, they must: 1) perform adequate molecular screening methods for Chlamydia at both donor and recipient sites; 2) implement risk mitigation strategies that avoid transmission of Chlamydia genotypes that are not enzootic to the recipient site; and 3) assess and mitigate risk associated with potential transmission between koalas and livestock. Standardised and comprehensive veterinary procedures are crucial in the assessment and management of disease and infection transmission risk, and telemetric monitoring is essential for the post-release monitoring of both translocated and resident koalas at the recipient site and subsequent evaluation of programme success.