Research indicates that northern koalas (Phascolarctos cinereus) are ubiquitously infected with koala retrovirus (KoRV). There is increasing evidence linking KoRV with neoplasia and a range of disorders associated with immunodeficiency, conditions observed at high rates in captive colonies, and sick koalas presenting to wildlife hospitals. However, less is known about the occurrence of these putative KoRV-associated diseases in wild populations. We analysed health data collected at the veterinary examinations of 691 koalas inhabiting three monitored wild koala populations in southeast Queensland between 2013 and 2020. At initial presentation, neoplasia and AIDS-like syndrome were detected at a prevalence of 1.16% (8/691; 95% CI 0.5–2.19%). Longitudinal data from koalas recruited into the monitoring programmes and receiving one or more subsequent examination revealed an incidence rate of 3.5 cases/100 koalas/year (95% CI 2.35–4.9). These findings indicate that a relatively small proportion of the populations studied were affected by these putative KoRV-associated diseases. However, the impact on individuals was severe, with high associated mortality in the diseased cohort. Furthermore, northern koala populations endure multiple threats, suffering severe declines in recent decades. We propose that the significance of putative KoRV-associated diseases on these populations should be considered within this context and that further research into the interactions between KoRV and other drivers of decline is warranted.