The Roche Cobas 6800 CT/NG assay was compared to the Abbott m2000 Real Time CT/NG assay for detecting Chlamydia trachomatis and Neisseria gonorrhoeae in 714 specimens referred to the bacteriology laboratory at Geneva University Hospitals, between November 2017 and March 2018, and in nine external quality controls for molecular diagnostics (seven from QCMD Glasgow and two from UK NEQAS). For C. trachomatis, the sensitivity of C6800 compared to m2000 was 100 % (95 % confidence interval [CI], 97.5 to 100 %), the specificity was 99.1 % (95 % CI, 98.0 to 99.7 %). For N. gonorrhoeae, the sensitivity of the C6800 compared to m2000 was 100 % (95 % CI, 90.5 to 100 %), whereas the specificity was 99.7 % (95 % CI, 98.9 to 99.9 %). The C6800 CT/NG assay appears to perform with great accuracy the detection of C. trachomatis and N. gonorrhoeae.