Chlamydia is the most commonly notified sexually transmitted infection in Australia. Australian guidelines recommend urogenital screening in asymptomatic men and women, and rectal screening in men who have sex with men or women reporting anal sex/symptoms. International studies describe a rectal chlamydia prevalence in women of 5% to 21%. We found that in women at high risk of chlamydia, 57% (32/56) tested positive for rectal chlamydia. Of these, 97% (31/32) had concurrent urogenital chlamydia. Women with urogenital chlamydia were significantly more likely to have a positive rectal result (χ 2, p = 0.000). Neither anal symptoms nor reported anal sex were associated with a positive rectal chlamydia test. The recommended treatment of rectal chlamydia differs substantially from that of urogenital chlamydia, raising the possibility that Australian women are being regularly undertreated due to a lack of rectal testing. Untreated rectal chlamydia may increase the risk of persistent infection, reproductive tract reinfection, complications and transmission. Further work is needed to determine the optimal management of chlamydia in women.