Chlamydia trachomatis (Ct) is the leading sexually transmitted infection (STI) across Europe. In Italy, prevalence is low in general population; anyway, predominance of asymptomatic infections, passive voluntary reporting, variable diagnostic criteria and coding practices suggest for considerable underestimation, preventing assessment of real burden of disease and health intervention. We analysed data on female genital Ct infection registered in STI sentinel surveillance systems in Italy from 2005 through 2016 and found 3,305 women. Among them, those aged 20-24 years had the highest disability-adjusted life years (DALYs) estimation equal to 106.77 DALYs per 100,000-stratum specific population. Through the study period, incidence rate (IR) for female Ct infection increased significantly from 2.9 to 7.1 per 100,000 resident population. Besides, we analysed data on pelvic inflammatory disease (PID) sequela reported from the National Hospital Information system (NHIS) in the same period. We found 287 women hospitalised with concurrent PID and Ct infection. We recommend targeted screening programmes in women aged 20-24, definition of nationwide active surveillance system, standardisation of diagnostic criteria and ICD-9CM coding practices.