Background The oral microenvironment provides the conditions for the establishment of microorganisms not usually considered residents of the normal oral microbiota. Sexually transmitted microorganisms such as Chlamydia trachomatis can adhere to any mucosal surface and ascend to reach appropriate locations to survive and develop symptomatic infections. Materials and methods To determine the presence of C. trachomatis, direct immunofluorescence of this microorganism was carried out in 76 randomly selected patients attending a periodontal clinic during a period of 1 year. Samples from the gingival sulcus and the pharynx were collected for detection of C. trachomatis. Patients who attended the periodontal clinic were divided into two groups: those without periodontitis and those with periodontitis. For the purpose of performing other statistical analyses, all patients were also divided by gender and age. Results From the total of 76 patients, in the group without periodontitis, 61% were positive for C. trachomatis in the gingival sulcus and 63.4% in the pharynx; in the periodontitis group, 45.7% were positive in the sulcus and 40% in the pharynx. When we compared patients by gender or age, no statistical difference was found. Conclusions The prevalence of C. trachomatis in this group was 53.9% in the gingival sulcus and pharynx of the studied patients.