Chlamydial infections are a major cause of morbidity and mortality in koalas in South East Queensland and Northern New South Wales. Infections are usually associated with conjunctivitis (blindness) and infertility in female animals and just like human infections are considered to be predominantly a female problem. However many male koalas are PCR positive for chlamydia, mainly C. pecorum and chlamydia can be isolated from many parts of the male reproductive tract in these animals including the testis, the epididymis and the prostate. Semen collected from these animals is also PCR positive for chlamydia in many cases. Similar to findings in humans and mice, sperm from infected male koalas show signs of DNA fragmentation, which is likely to compromise fertility following either natural mating or the use of banked sperm for artificial insemination. Based on these findings we are exploring methods to clean semen of chlamydia prior to preservation in order to maintain high quality sperm banks as a resource to maintain and/or rescue species genetic diversity. Our group has also developed vaccines for both female and male koalas and the effect of these vaccines on chlamydial infection of the male reproductive tract and subsequent sperm quality is being investigated as an alternative to antibiotic treatment. A multidisciplinary approach to studying the effects of chlamydial infection on fertility in male koalas is required to protect the future of this iconic native marsupial and studies in the koala have the potential to provide important new insights into how chlamydial infections may compromise human male infertility and potentially male infertility in livestock species such as pigs and cattle.