Abnormalities within the female reproductive tract of koalas (Phascolarctos cinereus) have long been recognised. During a retrospective study of koala health with Wildlife Health Surveillance Victoria, nine adult, female koalas were identified at necropsy with abnormalities within the genital tract. Gross findings included cystic and papillary structures within the upper genital tract (ovaries, periovarian tissue and oviducts), thickening of uterine horns, as well as mammary masses within the pouch. Samples were collected for histopathology and neoplastic lesions were evaluated based on WHO classification of ovarian neoplasia in human medicine. Histopathology of the ovaries revealed the presence of ovarian cysts (1/9), papillary hyperplasia (1/9) and cystadenoma (1/9), borderline tumour (3/9) and carcinoma (1/9). Carcinoma also appeared to arise within the fallopian tube (2/9). In most cases (6/9), extensive fibrosis containing distorted and cystic endometrial glands was observed within uterine horns, along with mild to moderate chronic inflammation within the uterus and/or cervix. The masses observed within the pouch were consistent with mammary adenoma and lipoma. PCR from cloacal swab revealed the presence of Chlamydia pecorum in one case and PCR from spleen was positive for Koala retrovirus (KoRV) in four cases. The histopathological findings of benign changes observed within the upper genital tract are similar to those described in the literature. However, our findings suggest that malignant neoplasia is part of the spectrum of pathology within the koalas’ female reproductive tract. Chlamydia infection has been associated with chronic inflammation and fibrosis within the uterus leading to cystic changes within the upper genital tract. Failure to detect Chlamydia sp. in the majority of these cases could indicate intermittent shedding or resolved infection. Interestingly, all animals displaying carcinoma were positive for KoRV. Further investigations should be performed to identify possible association between the presence of these agents and the development of malignant lesions.