Background: This study evaluated the performance of the BD ProbeTec Chlamydia trachomatis Q (CTQ) Amplified DNA Assay on the BD Viper System with XTR Technology in a multicenter study. Methods: Specimens were collected at 7 geographically diverse clinical sites from 1538 women and men attending sexually transmitted disease, family planning, and obstetrics and gynecology clinics. There were 1465 evaluable participants, 993 women and 472 men. CTQ assay results from female endocervical, self-collected vaginal, male urethral swab specimens, and male and female neat (unpreserved) urine specimens as well as those obtained using the Urine Preservative Transport (UPT) tube for the CTQ assay were compared with patient-infected status (PIS). PIS was determined based on the combined results from Aptima Combo 2 and BD ProbeTec ET CT Amplified DNA Assay. Results: The sensitivity versus PIS for endocervical, vaginal, and both female urine samples was 91.3%, 96.5%, and 93.0%, respectively. The specificity for the same specimen types was 98.3%, 99.2%, and 99.4% (urine neat) and 99.2% (UPT), respectively. The sensitivity versus PIS for male urethral swabs and both male neat and UPT urine were 92.1% and 98%, respectively, with specificities of 98.4%, 99.2%, and 98.1%, respectively. Conclusions: The CTQ assay demonstrated performance characteristics comparable with other commercially available nucleic acid-based tests such as Aptima Combo 2 and BD ProbeTec ET CT-Amplified DNA assay. Vaginal swabs and male urine specimens, the sample types recommended by the Centers for Disease Control for chlamydia screening, both performed at least as well as other sample types evaluated. © 2011 American Sexually Transmitted Diseases Association All rights reserved.