This was a cross-sectional study aimed to determine the prevalence of and to identify risk factors for Chlamydia trachomatis (CT) among human immunodeficiency virus (HIV)-infected women attending the acquired immunodeficiency syndrome (AIDS) clinic in the city of Manaus, Brazil, in 2009-2010. Participants answered a questionnaire containing demographic, epidemiological, and clinical data. A genital specimen was collected during examination to detect CT-DNA by hybrid capture, and blood samples were taken to determine CD4+T and HIV viral load. There were 329 women included in the study. Median age was 32 years (IQR = 27-38) and median schooling was nine years (IQR = 4-11). The prevalence of CT was 4.3% (95%CI: 2.1-6.5). Logistic regression analysis showed that age between 18-29 years [OR = 4.1(95%CI: 1.2-13.4)] and complaint of pelvic pain [OR = 3.7 (95%CI: 1.2-12.8)] were independently associated with CT. The use of condom was inversely associated with CT [OR = 0.39 (95%CI: 0.1-0.9)]. The results showed that younger women who did not use condoms are at a higher risk for CT. Screening for sexually transmitted infections must be done routinely and safe sexual practices should be promoted among this population.