Numerous bacteria, including Chlamydophila pecorum and Chlamydophila pneumoniae, are known to occur in diseased sites in koalas. In the present study the significance of such organisms was investigated by demonstrating their distribution in situ, in tissues collected opportunistically from wild koalas. Chlamydiaceae were demonstrated in epithelial cells and macrophages in association with pyogranulomatous pyelonephritis (8/11 kidneys), focal interstitial nephritis (3/21), and active inflammation and fibrosis of the entire upper female reproductive tract (10/10). In one case of pyelonephritis, Gram-positive cocci were also demonstrated in association with Chlamydiaceae and, in another, haematogenous filamentous bacteria appeared to be the sole aetiological agent. Three cases of chlamydial metritis were also superficially co-infected by a mixture of other bacteria. Chlamydiaceae were also demonstrated in pulmonary alveolar macrophages and epithelial cells in association with pneumonitis, and in hepatic and splenic macrophages in one koala. The study illustrated the prominent role of Chlamydiaceae in renal disease and disease of the uterus, uterine tube and ovarian bursa, with implications for pathogenesis and therapy. In addition, macrophages appeared to be a potential site of latent persistence from which systemic spread of infection might occur.