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Background In Cuba, little is known regarding the prevalence of Chlamydia trachomatis(CT) infection in adolescents and young people. We study the frequency of CT infection in these populations, and its association with clinical-epidemiological variables.Methods A total of 496 individuals aged 12 to 24 were recruited from November 2018 to November 2019. Of them, 302 were patients attending at sexually transmitted infections (STI) services and 194 were young volunteers. CT detections were carried out by real-time PCR and IgG serology.Results The prevalence of CT using PCR was 9.1% (45/496); 12.3% (37/302) for subjects attending STI service and 4.1% (8/194) for young volunteers, being significantly higher in the first group (OR=3.25; p=.001). CT IgG antibodies was detected in 38.6% (81/210). Individuals from 12 to 17 years old were more likely infected with CT (OR=2.21; p=.010). Infection was associated with the early onset of sexual intercourse, the frequent changing of sexual partners and black ethnicity.Conclusions The results suggest that Cuban adolescents and young populations are at highest risk of acquiring CT infection and developing reproductive complications. The data obtained advise the needs of implementation of a routine CT screening strategy, for timely diagnosis, detection and treatment at the earliest ages.