BackgroundChlamydia trachomatis (C. trachomatis) is the most frequently reported sexually transmitted infection (STI) in developed countries, but there is a lack data on its incidence and population dynamics in Spain. The objectives of this study were to estimate the incidence of C. trachomatis in patients seeking medical attention in an STI clinic with a defined population catchment area, to identify factors associated with this infection, and to explore differences between factors associated with new infections and re-infections. MethodsA retrospective study was conducted on a cohort of patients from a STI clinic who underwent chlamydia testing at least twice between 2007 and 2015. ResultsOf the 2633 patients who met study selection criteria, 795 (30.2%) tested positive for C. trachomatis at baseline (baseline Chlamydia). The overall incidence was 7.97/100 person-years (95% CI: 7.2–8.8): 5.9/100 person-years (95% CI: 5.2–6.7) among patients testing negative for C. trachomatis at baseline, and 18.3 person-years (95% CI: 15.6–21.5) among those testing positive at baseline. In multivariate analysis, the factors independently associated with overall incidence were a history of infection with C. trachomatis in the previous 6 months (hazard ratio=3.6; 95% CI: 2.3–5.4), younger age (HR <20 vs ≥35 years=5.5; 95% CI: 3.2–9.5), male sex, 2 or more sexual partners in the previous month and year, and inconsistent condom use. ConclusionsGuidelines should be established for C. trachomatis in Spain, including recommendations on the need for follow-up and re-testing, independently of age. Though data concerning the optimal timing of re-testing are inconclusive, our findings support the establishment of a 3–6 month interval.