Chlamydia trachomatis (CT) is the most common bacterial cause of sexually transmitted disease. It has been associated with arthritis and it is a risk factor for human papillomavirus (HPV)-induced lesions. There are few studies on the frequency of CT infection among systemic lupus erythematosus (SLE) patients. The aim of this study was to determine the prevalence of endocervical CT infection among SLE patients and evaluate whether or not CT infection is a risk factor for HPV-induced lesions. A cross-sectional study included a group of patients who fulfilled the American College Rheumatology criteria for a definite diagnosis of SLE and a control group of non-SLE female individuals from Bahia, Brazil. Polymerase chain reaction was used on endocervical swab specimens to test for CT; a gynecological examination including a cervical cytology and biopsy was done for the identification of HPV lesions. A total of 105 SLE patients were studied, and the control group was composed of 104 age-matched apparently normal women. The prevalence of CT endocervical infection was 3.0 % [confidence interval (CI) 95 % = 0.6-8.0 %] in the SLE group and 5.0 % (95 % CI = 2.0-11.0 %) in the control group; the prevalence ratio was 0.60 (95 % CI = 0.1-2.5). The prevalence of vulvar condyloma was higher among SLE patients (11.0 vs. 1.0 %, p < 0.001), as were the prevalences of low-grade lesion (12.0 vs. 1.0 %, p < 0.001) and cervical intraepithelial neoplasia 1 (9.0 vs. 1.0 %, p = 0.02). There was no association between the presence of HPV lesions and CT infections. However, the small number of patients with CT prevents a definite conclusion from being drawn. The prevalence of endocervical CT infection in women with SLE is low and similar to that of the normal population. This suggests that this infection has no role in the pathogenesis of SLE or the development of HPV-induced lesions.