The commercial BD ProbeTec ET (BDPT) system for the detection of Neisseria gonorrhoeae and Chlamydia trachomatis from clinical specimens was compared with our in-house LightCycler real-time PCR (LC-PCR) assays. Specimens initially positive by the BDPT system were retested by our LC-PCR assays. Our results for C. trachomatis testing indicate a 91.2% agreement when the results of 114 clinical specimens, initially positive by BDPT over a wide range of method-other-than-acceleration (MOTA) scores, were retested by our LC-PCR assay. The agreement between the two systems improved to 96% when only MOTA scores of >30,000 were retested by the LC-PCR assay. The overall agreement between the two systems for Neisseria gonorrhoeae detection from 155 clinical specimens was only 77.4%, with agreement particularly low (24.1%) for MOTA scores ranging from 2,000 to 19,999. Repeat testing of specimens with the BDPT only closely correlated with that seen by others demonstrating that reproducibility of the BDPT system for specimens initially within the MOTA score range from 2,000 to 9,999 is problematic, especially for Neisseria gonorrhoeae testing. With our study, we proposed an algorithm for C. trachomatis and N. gonorrhoeae testing which involves screening with the BDPT system followed by selective use of our in-house LC-PCR assays.