A total of 500 first-void urine specimens were tested for the presence of Chlamydia trachomatis and Neisseria gonorrhoeae nucleic acids using ProbeTec ET reagents on a Viper platform (BD Diagnostics, Mississauga, Ontario, Canada), Aptima Combo 2 reagents on a Tigris platform (Gen-Probe, Inc., San Diego, CA), and Abbott RealTime CT/NG reagents on an m2000 platform (Abbott Molecular Diagnostics, Des Plaines, IL). The performance of the three assays for detection of N. gonorrhoeae was comparable, but detection of C. trachomatis by the three assays showed more variation. All three platforms were suitable for the detection of C. trachomatis and N. gonorrhoeae, but additional factors, such as maximum daily specimen throughput, are important in evaluating automated systems for C. trachomatis and N. gonorrhoeae detection in high-volume laboratories.Chlamydia trachomatis and Neisseria gonorrhoeae are common bacterial sexually transmitted infections. These infections may remain asymptomatic, particularly in female patients. Untreated chlamydial and gonococcal infections may have longterm sequelae, including pelvic inflammatory disease, ectopic pregnancy, and sterility. The benefits of diagnosis and treatment are well understood. Since the introduction of nucleic acid amplification tests for the detection of C. trachomatis and N. gonorrhoeae in genital tract specimens, this approach has become the standard diagnostic method used in most laboratories. Moreover, urine has also been validated as an adequate specimen for diagnostic testing in many studies (4, 7, 11). We report here on the prospective evaluation of three automated systems for the detection of C. trachomatis and N. gonorrhoeae in urine specimens.A total of 500 first-void urine specimens were tested using ProbeTec ET reagents on the Viper platform (BD Diagnostics, Mississauga, Ontario, Canada), Aptima Combo 2 reagents on a Tigris platform (Gen-Probe, Inc., San Diego, CA), and Abbott RealTime CT/NG reagents on an m2000 platform (Abbott Molecular Diagnostics, Des Plaines, IL). The m2000 system is an automated magnetic sample preparation platform combined with homogeneous real-time multiplexed PCR for both C. trachomatis and N. gonorrhoeae (9). All specimens were tested according to the manufacturer's instructions.Each of the assays is designed to detect different targets. The primer sequences are proprietary, but the regions targeted are known. The Abbott RealTime CT/NG assays target the cryptic plasmid of C. trachomatis and the opacity gene of N. gonorrhoeae (9), the ProbeTec ET assays target the cryptic plasmid of C. trachomatis and the pilin-inverting gene of N. gonorrhoeae (11), while the Gen-Probe Aptima Combo 2 detects targets in the 23S rRNA of C. trachomatis and the 16S rRNA of N. gonorrhoeae (3).In order to increase the ability of the study to detect differences in performance between the three assay systems, an additional number of specimens positive for either C. trachomatis or N. gonorrhoeae were included among the 500 specimens. This approach allows th...