BACKGROUND There are no accurate data regarding the real prevalence of Chlamydia trachomatis infection in Spain. Our aim was to determine the prevalence of C. trachomatis infections and the risk factors for acquiring them among 1,048 young (15-24 years old) inhabitants of Laviana. METHODS The study was completed in the period between 1st November 2010 and 31st December 2011. We conducted a capture strategy in the whole population, instead of only in a sample group, with a capture conducted in schools, in the local health centre, by post and by phone as a last resort. The design was based on the model used by Shafer to increase screening rates. C. trachomatis was identified by RT-PCR in urine samples. RESULTS A total of 487 sexually active people underwent the test, which implies a response rate of 59.8% of the sexually active people (target population). The prevalence was 4.1% (CI 95%: 3.1-5.8): women: 4% ( CI 95%; 2.8-6.4) and men: 4.3% (CI 95%: 2.9-7.2). The circulating genotype was the E genotype. There was an increase in the risk of C. trachomatis infection when barrier contraceptives were not routinely used OR: 4.76 (CI 95%:1.30-17.36) p<0.05. CONCLUSIONS In our study the prevalence in women resembles those found in other countries in Europe and the prevalence in men is similar to that in women. Screening for C. trachomatis infection in women would be cost-effective in Spain given the prevalence of C. trachomatis measured by this study. The use of a condom is the best preventative measure for avoiding STIs in sexually active people.