Objective: The goal of this study was to determine the prevalence of C. trachomatis in women diagnosed with infertility attending the Outpatient Clinic of Infertility from Botucatu Medical School, UNESP, Brazil. Patients and Methods: This molecular study enrolled a total of 112 women. Among these patients, 62 presented primary infertility while 50 presented secondary infertility. The criteria for eligibility included women who were: reproductive-aged; no prior report of seroconversion for HIV; no antibiotic or vaginal cream used in the preceding 30 days; and abstinence from sexual intercourse for 72 hours before the visit. The women were submitted to a gynecological examination and cervical samples were collected with an endocervical cytobrush for molecular analysis of C. trachomatis. Results: The prevalence of chlamydial infection was 8% with similar prevalence between primary (8.1%) and secondary (8.0%) infertility. Conclusion: Considering the asymptomatic nature of chlamydial infection and its association with tubal factor infertility, there is a pressing need to incorporate the screening of C. trachomatis infection as part of the routine investigation for infertility. The early diagnostic by screening can minimize complications and reduce Public Health costs with Assisted Reproductive Technology.