Few studies have reported on sexually transmitted infections at the US-Mexico border, so the prevalence of Chlamydia trachomatis in this population remains uncertain. This binational project investigated the prevalence of, and risk factors for, C. trachomatis among women along the Arizona, US-Sonora, Mexico border. Women who self-referred for routine gynaecological care were invited to complete an interviewer-administered questionnaire and to undergo a Pap smear, C. trachomatis test, and HPV test. In 2270 women, C. trachomatis prevalence overall was 8.2% as measured by hybrid capture and 2.6% by enzyme immunoassay. Infection was associated with young age, a history of new sexual partner(s) in the previous three months, HPV infection, and proximity of clinic to the international border. Antibiotic use in the previous 30 days was associated with decreased odds of infection. Women in Arizona-Sonora border communities are at increased risk for C. trachomatis infection compared to women attending clinics in non-border locations.