Abstract Koala populations are in catastrophic decline in certain eastern Australian regions. Spanning from 1997–2013, a database derived from wildlife hospitals in southeast Queensland with N = 20,250 entries was classified by causes of morbidity and mortality. A total of 11 aetiologies were identified, with chlamydiosis, trauma, and wasting being most common. The clinical diagnosis at submission varied significantly over the observation period. Combinations of aetiologies were observed in 39% of koalas submitted, with chlamydiosis frequently co-occurring. Urogenital (cystitis 26.8%, bursitis 13.5%) and ocular (conjunctivitis 17.2%) chlamydiosis were the most frequently diagnosed representations of the infection. Approximately 26% of submissions comprised koalas involved in vehicle accidents that were otherwise healthy. Age and sex of the koala as well as season and submission period were compared for the case outcomes of ‘dead on arrival’, ‘euthanized’, or ‘released’ for the four most common clinical diagnoses using multinomial logistic regression models. Exploratory space-time permutation scans were performed and overlapping space-time clusters for chlamydiosis, motor vehicle traumas and wasting unveiled high risk areas for koala disease and injury. Our results suggest that these aetiologies are acting jointly as multifactorial determinants for the continuing decline of koalas.