To document the prevalence of Chlamydia trachomatis and Neisseria gonorrhoeae in the refugee population settling in Western Australia from 1 January 2006 to 31 December 2009 and make recommendations for future screening for chlamydia and gonorrhoea in the refugee population. A prevalence and quality assurance study of 2610 refugees aged 15 years and older who attended the Humanitarian Entrant Health Service in Western Australia and were screened for chlamydia and gonorrhoea. Demographic details and results of C. trachomatis and N. gonorrhoeae tests on first void urine. The prevalence of chlamydia was found to be 0.8% (n = 21) in the refugee population. No gonorrhoea infections were detected. The prevalence of chlamydia was low (0.19%-1.23%) when analysed by sex, ethnicity or age and was considerably lower than other subpopulations considered high risk in Australia. The low prevalence rates of chlamydia and gonorrhoea found in the refugee population suggest that current screening guidelines should be updated. We recommend screening all refugees who are sexually active up to age 39 years, taking into account an appropriate sexual history; otherwise, screening guidelines should be as for the general Australian population.