Background: A prospective, cross-sectional study was undertaken of pregnant women attending antenatal services in the remote far west of New South Wales, Australia, between October 2004 and May 2006. Of 420 eligible women, 218 (52%) participated in the study. Six women (2.7%; 95% CI: 1.0-5.9) tested positive for Chlamydia trachomatis. The prevalence among pregnant, Indigenous women (n ≤ 44) was 9.1% (95% CI: 2.5-21.7). Infection was significantly associated with Indigenous status (P ≤ 0.003) and self-perceived risk for chlamydia (P ≤ 0.05). Pregnant Indigenous women in remote areas may be at higher risk for chlamydia and targeted screening of this group should be considered.