Introduction: A prospective study was designed to assess the performance of the new CT OligoGen kit and the cobas 4800 assay for detection of Chlamydia trachomatis. Methods: A set of samples that included urine samples (n = 212), endocervical (n = 167), rectal (n = 53), pharyngeal (n = 7) and urethral swabs (n = 3). The samples were sent from a regional sexually transmitted diseases (STD) clinic in Seville, Spain, and were collected from 261 men and 181 women. Discordant results were re-analyzed and clinical data and other tests were reviewed in order to resolve them. Results: Sensitivity, specificity, positive predicative value (PPV), negative predictive value (NPV) and kappa value for C. trachomatis detection using the CT OligoGen kit were 98.5%, 100%, 100%, 95.4% and 0.97, respectively. Conclusions: This new kit had a high sensitivity, specificity, PPV and NPV for C trachomatis, therefore the performance profile confirms the usefulness and reliable results of this new assay. (C) 2015 Elsevier Espana, S.L.U. and Sociedad Espanola de Enfermedades Infecciosas y Microbiologia Clinica. All rights reserved.