The aim of this study was to monitor chlamydial shedding patterns in clinically affected koalas before, during and following treatment using quantitative real-time PCR. Swab samples were obtained from 14 koalas presented for treatment at the Australian Wildlife Hospital. Four of these animals were followed over a period of 8-9 weeks. Primers were designed based on the consensus signature sequence of the 16S rRNA chlamydial gene. Additional primers were designed based on the sequence of the koala beta-actin gene and used to normalize chlamydial values when comparing results from different swab samples. Chlamydial 16S rRNA gene copy number was highest in swab samples from clinically affected sites. Daily injections of chloramphenicol resulted in a marked and rapid reduction in the numbers of chlamydiae being shed from all sites. In general, chlamydial copy number was no longer detectable by the end of the 2nd week of treatment. No evidence of relapse of infection was detected at 2 weeks after the cessation of treatment. In contrast, topical chloramphenicol treatment of the eyes required a longer treatment period and had little effect on the shedding of chlamydiae from other sites of the body. Further studies are required to confirm the efficacy of a shorter treatment period.