Background: Genital Chlamydia trachomatis infection is a worldwide public health burden. A screening program for C trachomatis was therefore initiated by the public health insurers in Germany ("Gemeinsamer Bundesausschuss", GBA) in April 2008.Objectives: To estimate C trachomatis prevalence from screening 115,766 asymptomatic females and 20,033 female patients with unspecific abdominal pain. Study design: Urine samples (pooled by five for the asymptomatic screening subjects) and cervical swabs were analyzed using semi-automated real-time PCR. Infection prevalence was determined separately in four categories of women, defined by health status (asymptomatic screening vs. non-screening with unspecified symptoms) and test material used. Comparative analyses were stratified by age and pregnancy status. Results: Experimental evaluation of the assay used revealed a detection limit of 379 genome copies/ml urine. For pooled urine samples, the positive predictive value was 100% whereas the negative predictive value equaled 98.1%. The observed infection prevalence was higher for cervical swabs than for urine samples. Prevalence estimates also differed significantly between pregnant and non-pregnant adolescents (<= 20 years), irrespective of the test material used (10.2% vs. 7.3% for cervical swabs, 10.9% vs. 6.1% for pooled urine samples). Conclusions: Our retrospective study, based upon a very large number of females from all parts of Germany, revealed a high infection prevalence in adolescents, particularly in pregnant adsolescents, thereby justifying the screening directive of the German GBA. (C) 2009 Elsevier B.V. All rights reserved.